In my experiece Ati is better suited for FPS games and GeForce for flight sims. Had to say it.
Within the last few years, it more so depends on the developer. They usually sign agreements with Nvidia or ATI for their games and they gear their coding to emphasize the advantages of their drivers and hardware. I find that EA likes to do this quite a bit with their games.
Examples are games like Call of Duty, BF2, and Company of Hereos where they're geared towards Nvidia cards. A comparable Nvidia card will bench higher than an ATI card (maybe not a whole lot, but its there). I can't recall the last time I
played an ATI sponsored game, it was probably Black and White.
Just looking at some benchmark tests at Tomshardware, Assassin's Creed is more so dominated by Nvidia Cards. Crysis does well with ATI cards (depending on the setting) and is only beaten by Nvidia cards in SLI.