probably. PCI-E is going to appear in server setups first, and that's linux main market so I'd suppose that it's supported it out of the box for some time now. But I don't know that for certain since I don't have a board with PCIe.
However if you want to be sure Suse and Redhat have hardware certification stuff with Dell and HP and whatnot and you could check to see what machines they have that have PCI-E.
Some companies are more Linux-friendly then others.. Usually well supported are Via, Intel and especially AMD. Bad support comes from Nvidia and ATI.
For Video cards you'll have to check with Nvidia website to see if their propriatory drivers support PCIe operation. They have some forums that you can ask in that are nvidia/linux specific. Avoid ATI cards.
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