I did some stereo using IDV, here's my experience
I may be wrong, please correct and forgive me.
The stereo is generated by your video card via openGL
The movie is recoded via a QTime plugin.
The QT just can't record the stereo (no access to the frames, too much
pixels/second to encore)
The workaround is :
1 record your animation, say the left eye
2 shift your point of view by rotating your model, say one stroke on the
3 record your animation, right eye
4 put your two movies side-by-side using after effects or virtual dub
5 watch your movies using :
you can do some anaglyph encoding too :
I've removed the movies for i needed some space.