For some weeks GeoGebra 5.0 beta version now supports as well Java OpenGL 1 (JOGL1) and JOGL2 for 3D rendering. You can start both from webstart here:
Portable versions should follow.
Historically we started 3D with JOGL1. JOGL1 supports old graphics cards; JOGL1 is obsolete but can still be downloaded.
As a final release we may use only JOGL2, that is the current OpenGL for Java project. Unfortunately it’s not supported by all GPUs for now. JOGL2 is still in release candidate stage, so hopefully improvements will be done to correct this!
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Also http://www.geogebra.org/webstart/5.0/geogebra-50-no3d.jnlp is available: this will give a fully functional 5.0 version without any 3D support. If neither JOGL1, nor JOGL2 works on a certain workstation, this should still work with the most recent features of GeoGebra 5.0.