From what I understand, the Quadro cards are specifically designed to do stereo because they have a quad-buffer (hence the name Quadro?). This allows two hardware graphics channels using hardware double buffer for each channel (each eye is one channel). The GeForce cards are not quad buffered, and so you can't get double buffering per channel in hardware, and as such, performance is significantly decreased.
I have a Quadro4 750 XGL in my Slackware Linux 9.0 box, and the stereo works only with OpenGL Performer stereo specific apps. I think the reason they don't support stereo in Linux is because there is a need for a software emulation of the double buffers for each eye on GeForce cards. Ostensibly, there is not enough demand for Linux 3D gaming to justify the extra development effort on Nvidia's part to get that working.
That's just my guess.