For video cards, if it fits in the slot, it'll work, so yes.
A PCI 6200 would be the same speed as an AGP 6200 though, because it does not have the bandwidth requirements to fully saturate the bus. Basically, no bottlenecking. You only have to worry about this on faster cards.
Here is a little guide I made on overclocking video cards. http://computerforums.org/showthread.php?t=96527