On Windows, you can pack these files into your installer:
j3dcore.jar, j3daudio.jar, j3dutils.jar, vecmath.jar J3D.dll, J3DUtils.dll, j3daudio.dll
Load the DLL files with System.loadLibrary(), or set java.library.path appropriately. Same on Linux, only with *.so files.
I guess that it could be similar on Mac OS X. But I don't know if it's legal !
The Mac OSX version appears to have five or six jnilib and jar files and one replacement system file in it. When I tried loading Jav3D using just the jnilib and jar files, I ran into problems with programs which had a Canvas3D and some other component sharing a window--the Canvas3D would be drawn in the lower right corner of the window and the other window contents would not draw.
--Brad Vender
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