Much of the graphics applications are written in OpenGL, opengl have low level API due to which it makes life easier when compared to JAVA3D, Java3D is slow compared to OpenGL.
GL4JAVA is not compatible with latest Mesa 6.0, it will crash if u try to use it, this fellow is sleeping, and gave up as JOGL is picking pace. Some body said that GL4Java has lot of memory leak problems bcos of poor implementation of JNI calls, and it is very difficult to modify if u find a bug. If u got a problem then u are dead as no one will bother to ur question posted in gl4java forum or if u write to the author. gl4java is compatible with JDK1.4 if one day sun comes with JDK 1.5 then u may not find to use gl4java as I am not confident of the author that he will upgrade the codes.
JOGL is quite a good one, good use of patterns, not so complex,u can understand the source code, less memory leak problems, certain care has been taken.
Good forum there are people who are paid to help u out if u got any problem, once u post it on the forum.
SUN is going to maintain it that is a good news.
My experience
We have a very complex software developed using GL4Java and using Mesa 4.0, I have a defect which will be working only if I use Mesa 6.0 but if I move to Mesa 6.0, then my application crashes, I posted to get some help from the forum but no use. I tried asking the author but hopeless, In the end I changed my codes to use JOGL, not much difficult thing.
I sucessfully managed to fix the bug.
My Defect: I am using latest redhat version which uses gcc 5.0 and Mesa 4.0 is using