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 JOGL1 supports old graphics cards; JOGL1 is obsolete but can still be downloaded.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!