I wonder for my own use and curiosity, how popular is Java in indie game development , in 2d and 3d? Are there any good open/closed source games done in java?
Java is the language used for Android games. (I believe there may be some other methods like using C++ but its usually Java). If you have an Android phone, you can test the top-downloaded games to see good examples.
I think it's good for indie development - in fact I am doing an indie game for android. There are many tools that Google provides for you - such as debugger, emulator, memory allocation tracker. You can also use the Eclipse IDE with it.
There is also a lot of code online and the StackOverflow site if you get stuck on a bug. Also, Android supports openGL for 2D/3D games (though you can make a 2D game without it - as I am doing).
It's not terribly popular, in my experience. There's a few problems. First off, Java isn't the most efficient language around (though better than many think), but that lack of efficiency isn't really compensated for by ease of development. Second, running Java is kind of a pain - it's gotten better recently, but it's still tainted by Java's legendary growing pains. Third, Java hasn't had particularly good graphics support in-browser, and if you're outside the browser, you may as well use something else.
It's not really a matter of Java being bad. It's a matter of Java not being particularly good for any game-related niche, and other languages actually being good. The language that does everything in a mediocre fashion loses to the languages that do something well.
There's a list of famous Java games on this very site, but, well, you can see how popular it is.
Not quite answering the question, but javagaming.org has a non-exhaustive list of commercial Java games here.