I had the same dilemma 2 months back and went with a GTX460(PCIe 2.0) as i wasn't brave enough to try the HD6870(PCIe2.1) . They cost virtually the same over here . I couldn't find a return policy with my retailer so couldn't go for the AMD cards . But if you manage to persuade your retailer to accept a return if the card doesn't work you can buy the ATI card .
But listing your full PC specs and budget would lead fellow members to help you
If i remember correctly @iamthecrowe has a HD6850 working on a PCIe1.0X16 slot.
He also mentioned about BIOS upgrade and numerous reseating of his ATI card to make it work .