From my personal perspective, I'd go for nVidia for my own reasons. I have no DX9 games at all, other than DX9 plugins (Direct64, Pete's OpenGL2, Dolphin) and stuff, which aren't exactly that GPU intensive compared to say, FarCry (games which I don't really play). I have a few DX8 games that work well enough on NV hardware, but I play more games in OpenGL whenever there is an option to, and I have a *lot* of OpenGL games since I prefer the API over Direct X at the moment, although I don't use Linux. I'm really into id games such as Doom and Quake that I missed the first time around, I play both via Doomsday/glQuake/Tenebrae which are in OpenGL. SM3.0 would be irrelevant unless an N64 plugin utilised them, then it'd be useful to me.
I'm into classic console emulation, particularly N64, so MSAA would not be as good as some super sampling modes to alias those alpha textures, particularly with Jabo's plugin. I don't video encode so that is also a moot point. ATi cards can have issues with PJ64 with the current drivers (not sure how many ATi owners this affects, but there's a fair few) so they can't work in 32-Bit mode.
So, from this I believe that from what I like to do on my computer, an nVidia card would provide the best solution rather than an ATi card. It may not be even worth me upgrading for this generation since the card I have serves all my retrogaming purposes and more, so I'm happy. These 6xxx are likely to be too expensive for me to afford, so I'd even be happy with something like a 5900XT if it is cheap. Me getting an ATi would be simply idiotic since it's OpenGL is inferior to nVidia at the moment, less compatible with the emulators I enjoy playing, and has DX9 performance I'll barely even use with not one proper DX9 game on my PC. So I've weighed up the options and made a decision.