The PCI and PCI-E cards are very different. So it's not PCI/PCI-E. If anything, it's PCI/AGP and PCI-E.
However, all 3 cards types are essentially the same.
Yes, I know this sounds contradictory.
The PCI is the PRO 128, 7200 and 7500 cards only.
The AGP is the 7200 to 9800, so around a dozen or more models.
The PCI-E is the post-9000 cards, with the "x" in the model (x600, x1900, etc).
The PCI has Theatre 100/Rage chips.
The PCI-E has Theatre 200 chips.
The AGP has both (100 for 7000, 200 for 9000)
The chips essentially perform the same. The 200 has a slight boost to MPEG encoding quality, but it's negligible. (ATI MMC MPEG settings more important)
All are identical for AVI capturing.
The AGP cards have the best overall support by hardware and OS, while the PCI and PCI-E cards are more finicky.
I consider the 9000 series AGP cards to be better than the PCI express cards.