There are multiple things to look at. Check if the boards support DDR400, 8X AGP, however many PCI slots you want, however many RAM slots you want, USB 2.0 support, which chipset it has, which onboard sound it has, if it has onboard LAN, onboard SATA support, and if it supports the absolute best of processors for that socket type (AMD or Intel).
You know, to make this really simple, I'd just get either the Abit NF7-S 2.0 or the Asus A7N8X Deluxe if you're gonna go with AMD, and the Abit IC7 series if you're gonna go with Intel.
Those are the best motherboards for each type of processor...you don't need to look at anything else.
-Lasereth