First off, AGP and PCI-E are interfaces or slots that video cards fit into. They are different sizes, specs, and are NOT compatible with each other.
Second, your upgrade depends on two things:
1) What your motherboard currently supports now (PCI-E or AGP). If it is AGP, then get AGP. If it is PCI-E, then get PCI-E.
2) Or, if you want to go PCI-E(newer technology) and your motherboard does not have a PCI-E slot, then you have to buy a new motherboard. Then you have to worry about your current CPU, etc working with the new motherboard.
PCI-E does support a faster transfer rate between the vid card and the rest of the system. However, that's not to say that the vid card will even fill up either interface's bandwidth.
Intel E6750...........PSN: ELBATROP
XFX nForce 650i Ultra
Patriot PC2-6400 8GB (4x2GB)
36GB WD Raptor
Samsung SyncMaster 931c
Samsung SyncMaster 750s
Windows 7 Home Premium 64