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Having had experience of both, I would vote for NVidia. Some people claim the ATI drivers don't work at all, which was not my experience: they do, but they are a little bit of work to install, whereas the NVidia drivers are much easier.
One thing in favour of the ATI drivers: I was able to install ATI drivers for multiple kernels on my machine at once. By comparison, with the NVidia drivers, if I reboot using a different kernel, I have to reinstall the drivers.
One more thing in favour of the NVidia drivers: the ATI drivers seem buggy. I got lots of artifacts on the screen when playing Return To Castle Wolfenstein using my old Radeon 9600 Pro, which annoyed me. Also, Mozilla and Firefox used to randomly crash on me quite frequently. Since I swapped my graphics card to a much more powerful 6800GT, I have been able to play Doom 3 without seeing any artifacts, and Mozilla no longer crashes on me.
To summarise, I am of the opinion that NVidia have done a better job of their Linux graphics drivers than ATI have.
Nine times out of ten, nVidia will win the vote. That said, I've recently been playing Doom 3 + expansion pack on a Radeon 9600 Pro (gentoo system) without too many problems. Certainly this time last year, the game would die in about a minute flat with ATI's drivers but early this year, they did just enough to get things going properly. Performance is not nearly as good compared to Windows but that's partly down to ID/Zerowing's port of the game. The Doom 3 engine is a useful benchmark because not only does it use fairly modern shader techniques, it's also likely to crop up in numerous other games.
(One point about Doom 3: it seems to think my card is v. low spec and turns EVERYTHING right down, making it look pretty ugly. You need to ignore the recommended settings and crank stuff up or the game's just not worth playing.)
Unreal Tournament Demo (can't recall exactly which version but it's from last year) runs pretty well too, Tux Racer and my own forays into OpenGL seem fairly ok these days too.
That said, I don't think I've ever had more problems with nVidia's drivers and cards. They install easily and perform well.
So I'd say if you want to play safe, go with nVidia but if you spot a bargain ATI card (they've often been the better bang for buck in recent years and generally run a fair bit quieter) then don't be too afraid to take the plunge ... but keep the receipt!
Whatever you consider, search around for people's opinions on that specific card as you mileage may vary from model to model.
under linux Nvidia cards and drivers just work as they do in windows.
ATI cards have issues with drivers both in windows and linux, not to mention the 3d support for ATI cards is pathetic in linux. to top it all off ATI has flat out stated they refuse to put more effort into making good linux drivers.
Just to let people know - while I agree that NVidia is far better for Linux, the newest ATI drivers were a breeze to install for my Radeon 9550, run the drivers as root, run the X config program it tells you to, and restart the server. Thats all there was to it, so ATI may be a viable contender for graphics on Linux.