I always found that NVIDIA's Physx software made my games run more smoothly. Because games like BFBC2 or games running the Source Enginge, need a lot of physics calculations, having an SLI setup where one card would be a physx processor made my games run really smoothly even with graphics on high settings. I also found that while AMD cards looked better on paper in terms of specs, when it came to actually testing them out, NVIDIA was more than competent. AMD cards can run the same games on really high graphics settings as well, but when it came to physics calcualations the game would start to lag (Like when a building blew up in BFBC2, which wouldn't happen when using NVIDA cards with Phys-X).
Forgive any errors I may have made, I'm not exactly an expert in this sort of thing.