Java3D supports quad buffer stereo with opengl. You will most likely need a NVidea quadro graphics card and a way to connect it with a 3d display device.
Just pointing out that it could be misunderstood. ;D And what’s wrong with 3D? If I had 4 graphics cards in my computer and a 3D TV I’d probably play most of my games in 3D… I mean, as long as it isn’t abused and the tech is good I don’t see a problem with it.
You must also set up the nvideo driver correctly. There is a special setting to enable quad buffer stereo.
Also found there is a problem with Windows 7 and overlapping transparent windows. Stereo did not work when the top of the start button overlapped the stereo canvas.