I believe that for a low end or a mid range graphics cards they are pretty much similar, when you go to the high end controllers you start seeing the differences.
I used nVidia GeForce in several PCs I have and recently got one PC with an ATI.
both work fine, but I am using basic AGP cards, and not the high end. the nvidia one I have sometimes has refresh problems with high resolution games, but it could be that it does not support the resolution of the game.
make sure to use AGP cards - those fit into the Advanced Graphics Processor slot (AGP) on your motherboard and thus can work faster with the PC bus.
The ATI Radeon 9800 XT is considered a good high performance card.
you should also identify what are your needs in terms of functions such as TV out, DVI, etc.
