Historically network and graphics drivers (and maybe sound?), and sleep mode were the things to check for Linux support. These days, all three major graphics manufacturers have Linux drivers, and I haven't heard any problems with networking for a long time. Sleep is probably still an issue... And most everything is already included for you (networking, sound, graphics) on the motherboard. So just check how good Linux support is for the motherboard you'd like to buy (and any PCI cards you'll add, if any).