I am actually working on my own game IDE/platform at Play My Code; so here is my opinion based on the experience of building that. First I am using HTML5/JavaScript/Canvas for the front-end and PHP for the back-end. I plan to use WebGL in the future, but still only supporting 2D, so I have the canvas as fallback. On the server I plan to switch from PHP to Java; Wordpress and my current hosting are the only things holding this back.
If your aim is to be fully in the browser, then I’d recommend HTML5 + JavaScript. Otherwise Java is a good choice. For the back end I wouldn’t advice JavaScript; it’s not quite mature enough for my liking (but it is certainly getting there). I’d recommend cheap PHP or Ruby hosting for now, and switch to something better in the future.
I’d advise against using WebGL, unless you can fall back onto the canvas (i.e. your building a 2D game). IE 9 doesn’t have WebGL support, but it’s canvas implementation is very fast and easily the best. There are alternatives you can use to get WebGL support, including a Java based one which will work in IE 6. However it’s very common for these fallback technologies to be incomplete or buggy (like Flash canvas implementations, or the WebGL canvas), so I’d advise you don’t use them. That means if you want 3D, either keep it simple (canvas is more then fast enough for a cheap voxel-render or raycaster engine), or use Java.
The main problems I have with Java applets are the startup time, caching bugs, it’s blocked in Chrome, a current issue where applets constantly flicker in Mac OS, and lots of small niggling issues you have to work around. An example of the last one are things like handling the user using an out of date version of Java, because it will simply crash with no error (this affects a HTML game too, but in my opinion it’s easier to work around). I’ve seen plenty of Java games randomly fail to start, or have other bizarre bugs. I have spent most of my programming experience working in Java, which is partly why I have applets fully blocked in my browsers. With HTML/JavaScript you will also have the option of re-using much of your code if you ever target Android or the iPhone; where as you wouldn’t have that option with an Applet. With a HTML solution you will also have better integration between the game and the surrounding web page (for example making the canvas fullscreen and fading out the rest of the page when the game plays, or interacting with forms). You can call JavaScript from a Java applet, and it’s straight forward, but Java-to-JS is not as simple as pure-JS.
You also get cross-browser bugs with both HTML and Java; I find HTML tends to have a lot more, but they are typically minor and easy to fix. With Java it is possible to make an applet which runs at 60fps on Windows 7, crawls at 1fps on XP and Linux, and crashes the entire browser on Mac OS. That said the Canvas is far from stable; I have had to write lots of browser specific code and workarounds in FireFox, Chrome and Safari to solve canvas bugs (IE 9 is the only browser where I have never found an issue). Your game will also be limited to the speed of the slowest browser it will run on (FireFox).
On the flip side Java is very fast, is a much more mature language, has the best tools available I have ever used, scales much better (proper module system through packages, proper multiple file support, and classes are nicer to work with then prototypes), works in IE 6 to 8, and you can use 3D in all browsers.
You also asked about the future; 1 year away I would expect canvas and JavaScript to be significantly faster (especially in FF and Chrome), WebGL to be properly out and supported in all non-IE desktop browsers, Apple to be talking about WebGL on the iPhone (it’s already coming in iOS 5, just not allowed for web content), and for Java to be blocked in more places then it is today (Java is consistently cited as a major security hole). But despite all the negatives I’ve said about Java above, I do believe that it IS the better platform. It is just that it requires LOTS more work. HTML/JavaScript is the easy option, and that is why I recommend it, because ultimately what you build is more important then the technology you used.
). Too with JavaScript language can programming in Server-Side with Node.js(http://www.nodejs.org) and sure cross-platform(Windows(Microsoft have plans allow developers create programs with HTML5, JavaScript), Linux, Mac, Android, iOS, …).