If you NEED to build your computer right now.. then stick with AGP. The PCIe boards, there are only a few, are hard to find and are expensive. Same with the cards. Also, the new technology is just still that... too new. It's not really been optimized and truly accepted industry wide yes (it will get there). Because of all that, the PCIe cards available aren't really any faster then any of the AGP cards. The price for the PCIe cards and boards are way up there tho right now. For something that is more expensive and has equal or, in a lot of cases, worst performance I would stay away from...
Now, if you can hold off.. I would really recommend building a computer in about a year. I would get something plain and simple for now to get you by for your computer needs. Something inexpensive and not extravagent. In about a year, this is what I'm going to do, PCIe will more then likely be the mainstay. More cards, and support for the technology will be around and more optimizations that will really allow this techonology to shine as many are predicting. By then, you'll see a MAJOR difference in performance I would think. Talking like the difference from going from PCI to AGP for video cards in the first place.