PCI Express is the highest end port. AGP is still alive, sort of, but everyone is moving to PCI-Express.
The high end cards are now only on PCI Express. And they went back and put a lot of the low end. Video cards only go into the X16 slot, the other ones are for different things, some motherboards support SLI, which means you can get two video cards and hook them up. ATIs is crossfire, which is basically the same thing.
If you have a PCI Express video card, you know you are doing well.