The architecture can make a board faster, along with a good chipset that supports lots of features, SATA, AGPx8, Wi-Fi, Dual Channel, DDR2 main memory...
Also, as a lot of builders know, the layout of the board means a lot. Sometimes the AGP card can get in the way when you try and remove a stick of RAM, you have to remove the VGA card first.
You should also check what you get bundled with the board, some boards bundle Norton Anti-virus/Internet Security 2004... also check to see if you get round IDE cables and round Floppy cables...
There is a lot to check when getting a motherboard.
[size=0.5]Full Aluminium ThermalTake Case
AMD Athlon XP 3200+ *400 FSB* Barton (2.2GHz)
ThermalTake Volcano 11+ Xaser Edition Air Cooling
1024MB Corsair TwinX XMS 3200 (Dual Channel 2x512) 2-3-2-6
256Mb XFX 7800 GS EXTREME
2x WD Raptors (10krpm 8MB Cache) 36.7GB using RAID -0
Video Logic SonicXplosion 5.1 Soundcard[/size]