PCIe, schmPCIe@ 2004/07/07
PCIe is a point-to-point system versus the simple shared-bandwidth PCI parallel bus, so x1 PCIe cards will in theory be faster than PCI cards, but there's really no reason to get excited about them, especially since there are bugger-all of them on the market at this point.
So, basically, early PCIe Athlon Whatever boards will, in use, be little different from PCI/AGP boards. They'll probably have those little x1 slots that you likely won't be able to use for anything, and will probably have fewer PCI slots as a result, and there'll be that really fast x16 video card slot that accepts a somewhat more expensive graphics card that ends up running only marginally faster than the cheaper AGP 8X version of the same thing. Sure, you'll be able to upgrade, and all, but you know that by the time a twice-as-fast video card and twice-as-fast CPU have come out, your mobo will be in some other way incompatible - unable to run the RAM fast enough, for instance.
Assuming money is no object, it's just about worth your while now, performance-wise, to upgrade from what you've got at the moment to the fastest A64 and new-generation ATI or Nvidia card on the market at the moment. You could confidently expect at least a 1.5X performance improvement from doing that. If, of course, money is an object, and if you're not actually whipping your current system to death, it's a lot more sensible to sit about for a while, let the Socket 939 mobos increase in number and get their bugs worked out, and then, maybe, get a PCIe board, if something decent's available.