PCI express vs AGP

We are trying to decide between two computers. One has an Nvidia32 APG card and the other has an ATI 64mb PCI express. (Both systems will ultimately have a VGA monitor attached to it.)

The PCIexpress is cheaper, but we have never used that knid of card before.

Is there a considerable difference between PCIexpress and AGP? This is on a new computer, so I’m sure the OS will work fine. Basically I’m concerned about the applications that are loaded after. Can the video card effect applications loaded on the computer? There are some old apps and I don’t want any conflicts.

Thanks for any advise.