I've been working with GL4java for about 2 months now and Java 3D for a few months before that.
Java 3D is good if you don't want to spend too much time doing low-level 3D stuff, plus the fact that it uses a scene-graph makes it easier to understand, in my opinion, than GL4Java. The problem that made me switch was Java3D has no Mac support yet, which seems to me to defeat the purpose of Sun doing a 3D package in the first place. There are versions for both OpenGL and DirectX with Java3D.
GL4Java is a straight port of OpenGL to Java, meaning anything you can do in OpenGL, you can do in GL4Java. It supports all OS's, as far as I know. Also, its like learning 2 things at once, since once you get the hang of it in Java, you can turn around and port it to C, C++, etc... with very little effort. The downside is that you have to code more because it's a stright port and doesn't offer the nice utility classes Java3D does. However, there are a lot of OpenGL tutorials out there to teach you how to do these things, so if you're up to learning it, I'd recommend GL4Java.
Let me know if you need any help.
Hope this helps with your decision
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MarsChelios