OK, well that’s quite a bottle of worms. Perhaps the single best one stop shop is http://gpgpu.org/
But yes GPGPU can be as complex as the effects of batch size and coherence on performance, or as simple as treating textures as 1d, 2d, or 3d arrays.
Is there anything in particular you are interested in doing?
[quote]Or even information if this is possible with the current version of JOGL.
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GPGPU with JOGL is the exact same as GPGPU using plain-ole OpenGL, only difference is that it can be easily run on any platform. Now with that taken care of, you need to start looking into how GLSL works. Usually GPGPU work gets done in fragment programs but there is nothing stopping you if either vertex programs or geometry programs location in the pipeline better suites your work.