They're just different

interfaces. PCI was quite common in the old days (5+ year ago)
for graphics cards. Then it was replaced by something called
AGP interface which is dedicated channel for graphics cards.
It is faster than PCI interface but not too much. Now PCI Express
is coming into play. Buy AGP graphics cards now. If you have to
buy a PCI graphics card due to some reasons that's also fine.
No big deal except you lose one PCI slot.