PCI-E has a lot more bandwith over AGP, plus if you go for Nvidia you can run 2 cards in SLI
PCI-E is replacing both PCI and AGP
it is basically the same thing as PCI, except that it runs serially (like what they did with SATA) which give a higher transfer speed
PCI-E 1x slots are for (future) average expansion cards, and 16x is for graphics cards