there are some exceptions, like I know there is a mobo with both PCI-E 16x and AGP slots, but it performs like junk..... there is an AGP->PCI-E converter card, but it only works with a couple of AGP cards....... simple answer: AGP mobo, AGP vidcard; PCI-E mobo, PCI-E vidcard....
Edit: To clear up your confusion, PCI-E 16x is an AGP replacement, not even close physically let alone electrically