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3D Simulations in Java

I have never done any 3D programming and will be working on a 3D aircraft crash simulation. I am going to do it in Java, though I know C++ is probably more popular for this sort of thing, but I have no experience with it and a limited time frame.
Could anyone recommend any engines or wrappers? I know there is Java3D, but isn't it getting a bit old now? I have also seen JMonkey Engine, although that is for games I am sure it would be fine for simulation software?
Thanks!

You're going to have to firm up your fidelity requirements before you're going to get a truly useful answer to this. Some observations:
Java 3D - It doesn't appear to have had much active development since 2008 (though it looks like it's been ported to use JOGL). If it does what you need, go ahead and use it, but don't expect it to get any new features anytime soon (unless you want to write them yourself). Since it's mainly a scene graph manager, it may be of use for display, but it doesn't have any physics simulation capabilities.
JOGL - This is the OpenGL bindings for Java. Its most recent stable version is also about 4 years old, but there are indications it's undergoing some development to take advantage of newer OpenGL features.
jBullet - This is a physics engine for gaming purposes. It's essentially a Java port of the C++ Bullet Physics engine.
jMonkey - This is a gaming engine, which combines both a rendering engine (Java 3D) and a physics engine (jBullet) into a single package.
Back to my main point. If your requirements can be satisfied with a game engine, then you're okay to go with something like jMonkey or if you want to strip it down, just use JOGL and jBullet.
The downside is that most physics engines used for gaming don't deal with aerodynamics so much as collision detection and constrained movement. There appear to be a few flight simulator extensions for jBullet, but I can't make any recommendations about their quality... I suspect they too are for gaming purposes.
If you want to start dealing with structural failure simulation for the purpose of engineering analysis and the like, you might be able to get these tools to do the rendering and at least a small part the physics associated with it. But a physics engine tuned for gaming is not well suited to this kind of analysis. For that you will need a professional engineering package, or a professional engineer with a background in aeronautics, mechanical engineering, modeling and simulation... and who knows how to program in Java.
As for
what happens to other aircrafts in the airspace, actions taken by
aircraft controllers and the debris field.
Most of this is not going to be included in any physics engine, even one suitable for engineering analysis. There's some aeronautics and mechanical engineering involved, but that only constrains what's possible. What you're talking about deals with human behavior under stressful situations. That's a focus of much research, but you're unlikely to find anything available either as open source or commercial software to satisfy that part of your project.
Bottom line, get a better understanding of your requirements. If you don't have that understanding up front, you're going to be solving the wrong problem.

Other alternatives are:
lwjgl (website) A gaming library including GL binding and support for controls and sound .
ode4j (website) A 3D game physics library. This is a Java port of the ODE C/C++ physics library.

Accessible, cross platform, relevant UI framework?

I'm an experienced PHP/JS developer with a tiny bit of background (read university projects) in Java/C/C++. I'm looking to branch out my skill set and would like some advice on what language would be the best to pick up, along with a UI framework for that language. I have a tiny bit of experience with Qt's C++ implementation.
Let me define what I consider to be "best". I'm looking for something cross-platform (I use a MacBook Pro and a desktop that dual boots Windows/Linux) that is reasonably easy to get into as far as UI goes but will be scalable to larger applications. I'm comfortable writing terminal applications in Java/C/C++/Python/PHP but some of these little things I've written I would be interested in extending with more user friendly/pretty UIs.
At the end of the day, I think this probably boils down to a framework discussion so, let's paraphrase the question as "What cross-platform UI framework is most accessible but also professionally relevant."

Well 3 are recommended:
Swing (Java)
SWT/JFace (Java)
Qt (C++)
Working with these UI toolkits is almost the same: (generally same approach, good UI designers, good communities ... etc) so the language choice should rely on what external libraries are you using and whether or not you want native look and feel for your application (Only Qt and SWT/JFace can give you native look and feel for your application, swing is very bad at it).

I like the Qt, it's easy to learn, easy to use, and is cross-platform and versatile enough to perform very well even on an ARM embedded device running busybox.

Have you considered wxWidgets? It's cross platform and there is multiple language bindings. It has been around for some time and is used in multiple commercial products.

Which platform to develop web-based game in?

I'm thinking of writing a new web-based game, and wondered if anyone had any suggestions on which platform I should opt for.
The game will be 2D sprite based, but will need to maintain a decent fps rate (there'll probably be up to 20 things moving at once). It'll all be controlled via the mouse.
I use .NET daily, so Silverlight seems a natural choice for me, but I want to make sure as many people can play it as possible...
Can Silverlight games be developed straight out of Visual Studio (I have VS 2008), or do I need additional software (and does it cost...)
What limitations does Silverlight have in terms of .NET version (can I use .NET 3.5 for example?)
What physics engines can I use?
Would Flash be a better choice? Are there free development environments for it (that are any good)? (I don't care about learning curve)
Is Java still an option?
So I just wanted some feedback on what's the best thing for me to use for a simple 2D web-based game.
EDIT:
can you provide more information? is
this single-player/multi-player? what
kind of genre? will there be a lot of
classical UI involved (lots of forms
with lots of button/checkboxes,
datagrids etc.)? will there be a lot
of animation and effects?
Single player game, with "attack waves" of enemies
enemies are only thing that move, player just points and clicks
no classic UI, just clicking on buttons (no lists / dropdowns etc)
minimal animation and effects, only graphical requirements are movement of enemies (which will require little animation)

I'm also interested in web-based 2-d games. I personally favor silverlight because:
I'm already familiar with c#/.net.
It has a lot of capabilities, even if it's not as many as full-blown WPF. I hear that LINQ alone is awesome for games. Local storage may also be a plus. There is a rich selection of controls you can use for the gui portions of your games. Honestly, WPF loses to silverlight in terms of interesting controls.
It's totally free. You need to download the silverlight toolkit for VS, but that's no issue.
One cool thing is that you can do full-screen displays. I also found it is fast enough (on my core2 duo laptop) to handle a decent amount of objects. The fact that silverlight is going to be a big part of winmobile 7 is also a good point (though we'll have to see how that turns out).
There are a number of silverlight games out there so you can see the possibilities.
http://www.silverlightclub.com/
http://silverlightgames.org/
http://www.silverarcade.com/
I suppose the main negative is portability and making people install "yet another plugin". Flash obviously has the broadest user base, but if your game is decent enough, people probably won't mind installing the plug-in. It's a painless install.
In terms of physics engines, FarseerPhysics that TomTom mentioned is most popular.
There is one other thing that I thought was really cool and compelling: http://www.codeplex.com/silversprite. From the website:
Run XNA games without code changes in Silverlight 3. SpriteBatch based graphics only, no 3D. Since the game compiles into straight Silverlight code, it will run anywhere that Silverlight can. [emphasis added]
The XNA-in-Silverlight approach is potentially really good (especially for more complex games that you might want to try profiting from) because that also opens you up to Xbox with minimal porting effort. However, I don't have any experience in that, so I can't comment further.
Edit in response to the OP's edit:
Since your game sounds even more simple than I had imagined, if you don't mind the learning curve or potential difficulties with doing a pure HTML+CSS+Javascript approach (which may in fact not be so great), I'm going to say maybe that's the best route after all. That's because of portability.
That said, I'm lazy and don't care if a few people miss out on my game, so I'd just stick to silverlight. =P

If you want maximum playability do it with all HTML and javascript and don't even use canvas and then the game will work basically everywhere, including mobile. You can balance what extra work that might cause you against developing for Flash or Silverlight and having a very limited mobile audience. You can check out processing.js as well.

If you want to go the HTML + javascript way, you can take a look at processing.js. It's a Javascript port (by John Resig) of the Processing language.
Pros:
Totally free.
Easy syntax.
Portability. No plugins.
Cons:
Still under development, some Processing functions (like the 3D functions) aren't ported yet
Also, check out John Resig's tower defense game in Processing.js.

IMHO Java is still an option, in particular JavaFX (http://www.javafxgame.com might be a good starting point).
However, your experience with a language/technology is probably more important than the choice of platform, so you should choose .NET (given that none of the suggested alternatives stands out so far).

As stated by Benny, Silverlight is a great platform if you're already familiar with .NET, and most of the tooling you need is built into Visual Studio (VS2010 has a built-in designer but the current RC version doesn't support the upcoming Silverlight 4).
One cool feature of Silverlight is its ability to utilize the GPU. This should provide a nice performance boost. I don't know if Flash offers this.
The Silverlight runtime is very small (under 5MB). And you can easily enable out-of-browser support, so that your game may be launched from a desktop shortcut, for instance, without the need for launching the browser (and being online). Silverlight 4 adds the ability to use elevated privileges (this gives you access to the native network stack instead of the sandboxed browser stack). With SL4 you also gain webcam support, if that's important to your games.

Silverlight MAY need additional tooling for Visual Studio, but this is a free download. Basically 2008 was made before silverlight, so you need to download the tooling for it.
Silverlight runs on a limited version - read the documentation.
I would in geneeral advice to go .NEt 4.0, Silverlight 4.0, Visual Studio 2010 - those are aruond the corner and you wil ldevelop longer han a month anyway.
Java - no sorry, why. I mean, theoretically yes, but if you are a .NET person, you have more knowledge there, siverlight is XAML (WPF similar experience, always nice). Why should you giv all that up for using Java?
Flash - DAMN, NO ;) Seriously ;) You dont want to deal with that unless you have to.
Physics engine - no idea. Need to check. Not sure there is a lot for it. Did you google? http://www.codeplex.com/FarseerPhysics comes up first.
I think it is a good approach. Silverlight is a small download to start - so, I dont think you loose too many people by it. I would do it.

Why are (almost) all the on-line games written in ActionScript (Flash) not Java?

I absolutely love good defender games (e.g. Gemcraft, Protector: reclaiming the throne) as they can be intellectually quite challenging; it's like playing chess but a little less thinking and a bit more action. Sadly, there are not that many good ones out there and I thought I would create one myself and share it with the rest of the world by making it available on-line.
I have never worked with ActionScript but when it comes to on-line games, this is the main choice. I have tried to find a decent 2D game in the form of a Java applet but to no avail. Why is this so? I could write the game, most comfortably, in Delphi for Win32 but then people would need to download the executable, which could deter some form downloading it, and also it would only work on Windows. I am also familiar with Java, having worked with Java for the last four years or so; although, I don't have much experience with games programming.
Should I not be deterred by the fact that all on-line games are written for in Flash and create my defender game as a Java applet, or should I consider learning ActionScript and games development for the ActionScript Virtual Machine (AS3 looks very much like Java... but still, it's an entirely new technology to me and I might never use it professionally.)
Could you, please, just answer the the question in the title? Why Flash, not Java applets? Is it only 'politics'?

Flash is more popular since its penetration rate is huge.
Flash is also more powerful when it comes to create and integrate graphics assets (since Flash CS* is also a vector animation editor).
It's also very easy to embed sounds and fonts assets, to play with bitmap effects, without using any aditional library.
And last but not least, there's a lot of sites who offers ActionScript APIs in order to earn money with your games by adding various ads in it (such as MochiMedia, Kongregate...)

Flash provides a fully-built graphics and sound engine that will handle separate objects ("sprites") on paths and animation.
In Java those features would need to be provided by third-party library. Java does provides the necessary building stones to build such an engine, however.
JavaFX might change this, however.

I can provide a little insight on the Java side: Early in the history of Java, Sun tried to push Java applets as the new way to display dynamic content in a browser. This attempt was doomed to failure by the combination of the following factors:
Java had (and still has) a lengthy load time for the (JRE) runtime;
Java originally had only AWT as a GUI toolkit, and AWT is limited and really ugly;
Java used to be a lot slower before the advent of faster CPUs and JIT compiling;
Java was (many think intentionally) supported very half-heartedly by Microsoft in IE, so it wasn't well integrated and ran poorly.
All this gave Java (deservedly) a horrible reputation, from which desktop and browser Java have still not recovered. To most people, Java stands for ugly, slow and often not working applications. It still suffers from this stigma today.
While both Java and Flash are Turing complete programmng environments, Java is more universal, with a bigger set of libraries for all kinds of different purposes. Sun strove to have the Java environment be universal among platforms, so browser-side Java includes a lot of libraries that are usually not needed. Again, more load time.

Simple answer: the flash player is installed in almost all of PCs, but JRE isn't.

Flash has a much wider install base, that can be the only reason. I personally don't install Java on my machines....flash, of course.
Why write something for a far smaller audience? I'm not saying it's wrong to, but that's usually the reason when you're making games for a profit.
Think of this equivalent with consoles, with the second generation playstation there were hardware add-ons available...but they were useless unless the games used them. You had 3 options as a game developer, package it with your product - driving the price up, assume they have it - smaller audience, or assume they don't - maximum audience, maximum profit. The result is the hardware never really sold much because as a game developer you had to assume they didn't have it.
For me, that equates that to Java vs Flash, if I have to install it, the price for me accessing it goes up...assuming they have the most common thing and you're safe, minimum cost of entry, maximum audience.
However, if you have a great game, I could be convinced to install :)

Flash typically performs better at the kind of drawing, animation and video features that games require, since that's what it was originally designed for. In addition, the strict-OO nature of the Java language does not lend itself well to the kind of ad-hoc rapid development environment that is common for games.
More importantly from an author's point of views, Flash is by far the more commonly-deployed browser plugin. Java just doesn't have the penetration on the desktop. Applets were historically despised for their instability and poor performance (particularly slow startup); whilst that has improved somewhat, Sun are continuing to undermine what user acceptance they have left with their obnoxious bundling updater. It is a brave company that develops anything much for desktop Java these days.
should I consider learning ActionScript and games development for the ActionScript Virtual Machine
It's definitely worth learning JavaScript/ActionScript. (They're almost the same language, sharing a standardised common core.) Then you can apply your Flash scripting knowledge to browser scripting. You can even consider implementing games in JavaScript/HTML itself!
AS3 looks very much like Java...
In as much as it's a C-like-language, yes. However the concepts and practice are very different; you'll have difficulty if you try to write JS/AS like Java.

A lot of flash developers are designers who have crossed over into making games. They used flash as a design tool before a programming tool.
Plus it seems to be something of a precedent now for online games to be written in flash so I guess people do not want to deviate from "the norm"

Future Flash CS5 could creates iPhone applications directly, so you'll be creating games for 2 platform at the same time.

Client Java vs (Adobe) Flash for web applications, what to choose and when

A few years ago client Java was unsuitable for web development because a remarkable part of web users did not have Java installed. ( I don't remember exact numbers, more than 10%).
Now I see the Google Analytics stats for a big site and it tells that >98% of users have Java installed.
Is these stats very biased by Javascript usage? As I understand Google Analytics measure only users that has Javascript.
Is the picture similar on other big sites?
Does client Java have really "stopper" drawbacks compared to Flash?
EDIT: I mean java applets mainly, java WebStart seems to be not suitable for average user.
I mention Javascript only to describe the way Google Analytics works.

When I wrote my diploma project, I had to choose between Flash and Java Applets. Here are some pros and cons:
Java Applets:
[plus] you program in Java, which is mature and stable
[plus] you can use the Java GUI frameworks that pack a lot of punch
[minus] the first time the user hits the page with the applet, the JVM must be initialized and this can take up to a few minutes even on a fast computer
[minus] Applets are not meant to be used as animation media; sure, you can do stuff, but it is like programming in C - you do everything from scratch
example: i needed to show a data packet as it moved between two routers. The packet must be a control of some sort, like a button or smth. This animation can be defined in 1 line of code in Flash, where all objects derive from some base object that can be animated. I could not find a suitable solution in Java.
Flash:
[plus] really really focused on animations;
[plus] ActionScript is actually an OO language
[minus] ActionScript is sloppy, bughish and has only a few supporters. If you are stuck, be prepared to search obscure Japanese forums for solutions
[minus] ActionSCript may be OO, but it lacks a lot of features, like Enums, fully fledged interfaces, threads (!!!!) etc.
[minus] Flash was designed to be used by non-tech people - they just use the authoring tool; I wrote code for everything and it worked, but it was a pain.
My conclusion:
I eagerly await a programming paradigm for animations and rich client interfaces.
ps: Silverlight seems to be a disappointment so far, maybe Microsoft will inject some $ into it.

Mmm, Java seems to be better supported than I though, I searched some stats and found between 92 and 96% of browsers support Java (ie. it is enabled enough to detect it! although I guess lot of Java detection algorithms use JavaScript to detect & report - as you point out - but JS support is very good too anyway, even more in our Web 2.0 era).
Adobe boasts better support, but overall the difference is rather marginal. Anyway, somebody really wanting to see/use the application will activate/upgrade/download the needed engine.
Now, we have to see what JRE is supported! Alas, I didn't found any stat for that.
There, Adobe have an edge: not everybody have Flash 9 or 10, but upgrading is quite fast. While downloading and installing a new JRE is quite a bigger task... Of course, you can target the historical lowest common denominator Java 1.1, or more realistically Java 2 (1.4), but it is still frustrating not to be able to use all 1.6 features...
I have seen some people complaining that Java applets crashes their browser (apparently on Unix systems) but it is more an issue with a minor number of browsers/systems than anything else.
And as pointed out, startup time of a Java applet is quite longer than for Flash (although some big Flash games are slow to load too).
Now, I have seen a number of Processing applets, like the notorious Webpages as graphs, most of them load quickly: lot of the power is already on the hard disk of the user, in the extensive Java library. Processing generates quite lightweight jars, while lot of Flash applets must include foreign libraries... or reinvent the wheel!

Some previous postings are obsolete in regard to comments on ActionScript. ActionScript3. became available in the Flex 2 time frame, i.e., January 2007 when Flex 2.0 and Flash player 9 shipped.
AS3 is a full blown OOP programming language comparable to Java. It has classes and interfaces, inheritance, access protection keywords for class members, constructors, statics, plus some nice things that Java doesn't have: properties, events, declarative data-binding, and closures.
By default AS3 is statically compiled, hence one declares the type of members and variables. This can be relaxed to where AS3 can revert back to dynamic typing ala JavaScript. It is less efficient at runtime, though. Sometimes when dealing dynamic data it is none-the-less useful to selectively employ dynamic classes. (A nice benefit of static type checked language is code completion in the Flex Builder IDE.)
Much of Flex development is accomplished using MXML. This is a declarative XML-based DSL for Flex. MXML gets compiled into ActionScript3 code, though. So what you do in MXML is equivalent to AS3 imperative coding, but can often be more concise, clearer, and more appropriately structured with respect to the underlying graphical Flex form it represents (i.e., MXML is good for coding the views of the MVC pattern).
The bottom line is that ActionScript3 programming of Flex is easy and natural for a Java or C# programmer to learn. The language is not at all the issue. The power of Flex comes in becoming intimate with the Flex SDK and the myriad capabilities found there.

Not an exact answer, as it would be very opinionated, just sharing my experience...
In a recent project, where we were building a WAI compliant site, we were asked to avoid flash objects as accessiblity was a major issue. Applets on a different note don't go very well with most web developers ;). One reason might be the differences in the paradigms of Rich UI vs. web UI.
However, we found applets to be irreplaceable (not speaking for .NET and ActiveX controls) when client side monitoring was needed. The application uses SmartCard based authentication and applets are loaded into browser to listen for client side events (card removal) and alert the server to end session.
In this context I tend to feel that Flash is meant to be eye candy (view) where as applet though designed to be versatile, takes the role of model on client side. It is to be noted that both applets and flash consume CPU cycles on client machine, hence were traditionally suited for tasks involving lengthy computation. Calculators, Report generators, Trend illustrators, Astrological chart generators (yes) and other tasks where data can be fed by user and are results shown immediately make use of these.
A major concern involves lack of client side software (Java, flash plugins). The user experience in such cases is more than annoying.

Noticed some comments about java not updating itself. Now 1.6.0_10 is out, and it's updating itself more easily and automated than before, and you have the option of a new install method, the java kernel one. This automates the install of java components as you need them.
Some text about this: http://java.sun.com/javase/6/6u10faq.jsp
So there are changes, Sun just wakes up with the new Ceo i think. I know it's 1-2 years until this new system propagates but you can start your project and have fun when it's ready maybe. :) Who knows.
Anyway, maybe you work +500% for easy animated features than flash, but if your app is not a simple animation, then you work +500% with flash for some simple 3 line java code substitution :) Depends on your app.

I worked in Java for the last 7 years, and then I recently started on AS3 on my newest project (1.5 years and going). I love AS3 and Flash, and here's why:
The language itself is very similar to Java. The documentation at Adobe is as good or better than JavaDocs.
The AS3 language supports XML as a native type. Parsing XML in Java is a nightmare.
There are nice animation and graphics frameworks for Flash, such as papervision 3D and tweener.
If you use the Flex 3 framework and Flex Builder 3, building interfaces that look as good or better than Swing is trivial. I loved writing UIs in Swing, but designing UIs in the visual Flex Designer is like a breath of fresh air.
I'm pretty sure that there's more browser support for Flash.
Have you ever seen a Flash applet load? It has really poor usability, and makes your user click through two or three dialogs before the applet starts. Flash apps just work.
Good luck on your project!