MoBos are going to continue to support AGP for sometime, depending on what MoBo you purchase.
PCI-Express, however, is where the future of gaming is. If you want a new system that has a good solid core, go for a PCI-Express compatible MoBo. You'll be solid for sometime, or at least until you hook up your next rig.
If you're lucky, and are willing to spend abit more, you can find PCI-Express boards that also feature 1 AGP 4x/8x slot.