I’ve been reading up on where Java3D is at, and in brief, the Java3D federation effectively concluded its work in 2008 but left it…unmarketed. The API was left complete, but interaction with the AWT and Swing libraries apparently left a lot to be desired…esp if you tried running it on OSX.
There are a lot of scene-graph libraries that use JOGL, which is a thinner wrapper around OpenGL or DirectX and apparently many people seem to appreciate this foundation more. jReality is the first project that I’ve spotted that clearly states it suggests being used for mathematical visualization.
Bitratchet 
3 responses to “Java3D, JOGL…jReality?”
The JogAmp community now maintains JOGL and Java3D.
History of the JOGL and Java3D transition 2009 – 2012:
http://labb.zafena.se/?p=656
The JogAmp community now maintains JOGL and Java3D
History of the transition of JOGL and Java3D into a community run project 2009- 2012:
http://labb.zafena.se/?p=656
Jogl is essentially a java wrapper around OpenGL, so will be low level and require to write shader code in order to do anything modern. Jmonkeyengine is probably more the sort of thing you’re after since it comes with a lot of prepackaged functionality (including its own IDE).