3D Vision has the most support between Nvidia and their mod community. 3D Vision is active.
The advantage of active is the resolution. Active displays generate 1920x1080 images for both eyes.
Passive displays generate 1920x540 images, which makes text very blurry.
The disadvantage of active displays is crosstalk, where you can sometimes seen a hint of the other eyes image. This is mostly an issue when there is high contrast between light and dark sections of the screen. I am not sure about passive, but from what I've heard, this is reduced.
Another advantage to active displays, is that they give you 120hz in 2D.