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Nvidia is the way to go if you're going to do PCI Express. Their binary drivers are fantastic! But, I would NOT recommend PCI Express. Do you know that almost every PCI Express card can work with the bandwidth provided by AGP 4x? AGP 8x is quite unnecessary as well.
The only reason you might need PCI Express 16x is if you were to store the caches on your system ram instead of the onboard ram on the card. This is a stupid marketing scheme as well. This won't speed anything up, it will just allow graphics card companies to cut costs while keeping prices the same, since they won't have to put so much ram on their cards. Though in the high-end workstation market, where cards have upwards of 512MB, this is actually a usefull technology. But you're not building a workstation. And I'm assuming you're running Linux. So why get a nice graphics card? If you want to run games, go Windows, because the DirectX API works best, almost exclusivly, on Windows. And if you are gaming on Linux, such as Doom3... well, go for the PCI Express if you have to. I'd stick with a AGP 8X board, just since AGP technology has been around a lot longer, is more stable, and better supported. And get an AMD because they work better at compiling and games. =)
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