Yeah, PCI-E is totally different. They say it's better, more bandwidth and such. As far as I know, there aren't any video cards yet that really take advantage of its potential, but it's been about 6 months since I looked into it.
Oh yeah, and there is that ability to run dualies like person said. Pretty much doubles your graphics power... assuming you have the $$$ to buy two vid cards.
Plus PCI-E cards are lots more expensive than their AGP counterparts.
I have a PCI-E on my mobo, but that's only because the mobo I wanted didn't have an AGP version.