Form Factor and Layout
Current popular motherboards follow the ATX form factor, but you can still find some Baby-AT boards out there. ATX is an improved AT design incorporating better design and a standard layout for I/O connectors.
The layout of the motherboard is important for ease of use and airflow. Room for large cards is important. It's a bit frustrating when a bank of DIMMs gets in the way of a Voodoo2 SLI setup. Check the placement of the CPU in relation to a case fans. Do the case fans direct air at the CPU or will the CPU's fan be working solo? Any motherboard following the ATX form factor should not have any of these problems, but not all manufacturers follow the exact ATX specifications- it doesn't hurt just to take a look.
Another factor to consider is the layout of the I/O ports, the floppy and IDE connectors. Are they easy to reach? Are they socketed with a key notch so there's only one way to connect the cable? It's annoying when you have to flip an upside-down cable because the motherboard manufacturer was too cheap to socket the connectors.
Also check for multiple fan power connectors. Many people are now using dual CPU fan setups in their Celeron 300A overclocking endeavors, making support for multiple fans a must. But enough about the externals. We're talking motherboards, what kind of features should I be looking for?