Well now that I think about it, if you plan on doing a SLI setup than yea, put several hundred bucks into some PCI-E. But if aren't doing SLI dont even bother really. Why? First, too expensive for what you get. Second, in SLI setup, each graphics card deals with the video processing for one half of the screen, so just a single PCI-E graphics card will pretty much equal out to AGP in normal gaming usage, however, SLI easily kicks AGP's ass. But it is also expensive, which goes back to number one. It is really up to you, but for my next rig, more than likely I am going for AGP still.
HTH