if there are any PCIe/AGP combo boards, they will be specialty hybrid designs similar to Asrock's Socket 754/939 combo. Unfortunately, in order to incorporate the large amount of logic necessary to do this, the boards will be pretty stripped down, just like with the dual socket boards. Don't expect nice features like tons of SATA ports, LAN, expansion slots, etc. Overall, it'll probably not be worth it. If you are looking for a mobo to last for a AGP and PCIe generation of GPUs, then you obviously will want a full featured, high end mobo, and you're just not going to get that with a combo design. Basically, if you are sitting on an AGP card, you are in one of the following situations: 1) You have a kickass card, i.e. 6800GT or something, in which case you should just sit on your current platform until you can upgrade both your mobo and video card 2) you have a midrange card, like a 9800 Pro, in which case you can easily sell it to a person looking for an above average upgrade (should be able to fetch like $150 easily on ebay) and use the money to get a PCIe 6600GT for even better performance (only like $175) or 3) you have a card that won't cut it anymore, i.e. 9600 series or below, and if this is you you should be getting a new card anyways, so why not make it a PCIe one? Besides, you can always pawn that old card on someone who needs something better than their integrated graphics or Geforce2 MX to play Sims 2 or rollercoaster tycoon, lol.
Anyways, as for PCIe in general, yes, it is going to replace AGP and PCI. PCI will coexist for a while, since most peripherals are still PCI, but companies like creative are already working on higher-bandwidth PCIe cards (creative has their new Zenith PCIe line of sound cards set for release in H1 05). Eventually, boards with no PCI slots will appear, but not for a while, kind of like how mobos had legacy ISA ports after PCI's introduction. AGP will transition more quickly, if for no other reason than that the graphics companies are gonna focus most of their production of new cards on PCIe, whether we like it or not. ATI's 5 new X800/X850 cards are all PCIe only, as will nvidia's NV41. The X700 and 6200 series are also PCIe only. The 6600 series is still overwhelmingly PCIe, although a few bridged solutions have crept in for AGPers. Anyways, the point is that unless you are upgrading within the next month or so, your best upgrade option WILL BE PCIe, because that's the way the graphics makers are structuring the market.