an AGP and a PCI-E version of the same model video card will have the exact same performance.
A 16x PCI-E Slot Has twice as much bandwidth as an 8x AGP slot, however, No video cards on the market come anywhere close to using that much bandwidth.
So, Technically, the PCI Express Technology is Superior to that of AGP, but there is currently no practical advantage for PCI-E over AGP in standard PC usage.
Now I *COULD* see some BIG advantages to using 16x PCI-E Networking to connect nodes within a Behemoth Cluster as opposed to how most are currently built using multiple nics each on 64bit/66mhz PCI slots. (Though the NICs would need to be a heck of a lot faster then Gig-E to use a full 16x PCI Express slot)