AGP and pci-e doesn't really matter because most games don't use up that much bandwidth anyways, just go for whatever interface card your mobo supports
oh btw, pci card are like, um, let's just say you wouldn't want to play games on them.
if u went to a shop to buy a computer right now, u could pick either agp or pcie n not worry about it.. I bought a system a month ago which was agp... thats just me.. If ur buying the computer to show off an shiz, go pci-e... if its just a computer then either is fine
If you want a PC that'll be ready for the newer games and graphics in the next couple of years (and can afford the associated equipment) then PCI-e is definetly the way to go. For a little cheaper and kick ass gaming for now you can always go AGP.