Suppose it depends on what you want to spend. I'd guess if you want a system compatible with the latest and greatest, go with PCX (I think that's what they are calling PCI-Express for short). Personally I just bought a new Motherboard with AGP. I was upgrading and already had an AGP card I wanted to use. Also the chipset I settled on only has AGP onboard and didn't have a PCX version yet (nForce 3 250Gb chipset for AMD64 processors)
AGP is no where near dead yet, but I guess PCX is the best you can get assuming you can find video card that supports it natively. I think it just comes down to price point, but I'm sure someone else will chime in with a more technical answer.