Meant to be Seen

I was wondering if any of you folks have any experience running stereo 3D on a system with a dual video card setup?

Would having two GPUs compensate for the performance hit 3D introduces, or does it not work that way?

At the moment only the nvidia driver supports dual GPUs, all the other drivers don't leverage the power of the 2nd card.
iZ3D and DDD are working on it though and th situation may change in the short term future. Until then I recommend you grab the most powerful single GPU card you can find : it will be more stable and more consistent with less bugs.

These cards are at the moment :
Nvidia Geforce GTX480
ATi Radeon HD5870

The nvidia one is slightly more powerful but it's also more expensive and uses much more power. It all depends on your budget.

Well , the GTX shines in minimum FPS department, so ...

Traditionally dual GPU (or more) and stereo 3d don't mix, even though it seems like they should. Nvidia now has dual GPU support of their 3d drivers but iz3d and DDD do not. Otherwise I would be running SLI myself. Best to just get a high end single GPU card like the GTX 480.