By default the MacPro will come with the ATI HD2600 but you can select a custom build and have the nVidia 8800GT installed instead. Alternatively you can buy third party cards, usually they're advertised as "Mac and PC Edition"
MacPro's uses PCIe cards. The problem isn't finding a cards that will fit in the machine. The actual problem is finding a card that has both the EFI ROM and BIOS onboard, this is basically required before the board will work in both the Mac and Windows environment (should you choose to enable BootCamp and install Windows.)
If you just wanna run WindowsOS on the Mac hardware, you can choose any card. However, booting into MacOSX requires a graphics card with EFI ROM, otherwise the system will just ignore your windows card will be completely and no video will be displayed.