^^No the AGP are cheaper than PCI-E. the BFG GeForce 6800 Ultra AGP is about $600 canadian and the PCI-E is about $740.
I think it matters when you plan on buying another computer/MOBO. it's true right now there isn't much diference between the two but in the future PCI-E will be better. So if you plan on upgrading again soon go with a AGP slot MOBO, but if your not going to upgrade your computer/MOBO for a long time go with the PCI-E. Thats just what i think