the general consensus about pcie vs agp is that the difference is yet to shine its pretty face. Theory and SLI is the only thing going for it--thats alot when thinking about upgrading though. But isn't anything to consider in your shoes--unless you are not dead set on your decision.
Somebody will ask why you want to build around a card and that it legit question.
Sell the card, take that money and go PCI-E and 939.