I build
my own PC. I choose the best hardware for Linux.
AMD: Because of their OSS initiatives.
GeForce: Official Linux driver that kicks ass.
nForce mobo chipset: Official Linux driver that's way cool.
If you're thinking about a soundcard (I'm happy with the integrated nForce soundcard anyway), choose one from Creative. They have Linux drivers.
ATi only tests their Windows drivers, they compile the Mac and Linux drivers with Windows code and without testing them. And even the Windows drivers aren't very good. VIA chipset mobo's don't have an official Linux driver.