I've got a 6600GT in my PC and have been very happy with it, the main diffrence I have found between it and my freinds ATI x800 has been support in games for diffrent nifty (water /fire /smoke) effects, (ie doom3 was optimised for nvidia cards yet I think half life was optimised for ATi) I know thieir not quite the same, diffrent OS and cards ect. To be honest all that happens is that you loose some of the really spangly effects but every thing else works nicely. Its going to be a while, if ever before the mac gets these games thats not really the issue. I reackon that the main issue you have to think about is what monitors you are going to run off them if thiers any chance in the future that you will be running two 30" Cinema displays you need to go for the Nvidia, the ati wont do two 30", "only" a 30" and a 23". However the ATi only takes up the agp slot but the nvidia's heatsink overlaps one PCI slot, rendering it unuseable.
I'd say go with the ATi so that you have more room for expansion at a later date.