i'm a 100% certified Nvidia fan, as far as Linux is concerned.
Nvidia pros......... far better Linux support. they have support forums, extensive help & faqs, & a dedicated developement team for Linux drivers. they supply easy to install Linux drivers which are updated regularly. extensive options for usage are available in the documentation. installation is generally a breeze, & if problems do crop up Nvidia is very good with supplying patches.
Nvidia cons........ ummm, can't really think of any.
ATI pros............ ummmm, they work fine if you can get them to work.
ATI cons............ basically everything opposite of the Nvidia pros i listed. developement for Linux drivers is very slow. new releases tend to take months to come out, instead of weeks, sometimes days for Nvidia. ATI in general has a very Windows like mentallity. they focus on MS users & just throw out some crumbs to the Linux community in order to keep them from forming a lynch mob, IMHO.
as for the boards themselves, performance wise.......... it's like Chevy's vs. Fords, to me........ just a matter of opinion as to which you like more. they both supply superb graphics & performance. i wouldn't say one is neccessarily better than the other in that department, if you compare boards with similar specs. the only difference is you gotta work to get ATI working in Linux, Nvidia just works.
the above are my personal opinions on this subject. please don't start a debate/flame war over which is better (Nvidia vs. ATI) here. i'm not dissing any ATI users. i've just had too many headaches with ATI vs. none with Nvidia in Linux.