What's Your Processor?
First and most important thing to consider when buying your motherboard - what CPU or processor are you using? Motherboards are made differently, not all motherboards will support all CPUs. What CPU you select will determine the type of motherboard you get.

For example, if you want to use an Intel Pentium 4 CPU, the motherboard you select must be able to support that brand and model of CPU. The motherboards are also designed to support specific speeds for a CPU, so make sure it can support the speed of the processor as well.

Choose Your Chipset
What is a chipset? Well, chipsets are the main controllers on the motherboard - they allow the CPU to interface with the various components and expansion cards installed.

When choosing your chipset, always bear in mind the type of memory supported by the motherboard. Make sure that the board supports the type and amount of RAM you need. Generally, choosing a chipset that supports high speed memory will allow your system to perform better.

Expansions Slots and Connectors
If you intend to various peripherals to the computer, then the number and type of expansion slots and connectors is important. By default, most motherboards these days have USB 2.0 ports incorporated into their design. If you do a lot of video capturing and editing, you'll also want to have a Firewire (IEEE 1394) port. If you intend to buy expansion cards, make sure the board comes with an ample number of PCI slots.

Do You Need to Overclock?
If you want to overclock your CPU (though I don't particularly encourage it) - you should ensure you get a motherboard that supports overclocking. You'll want a motherboard that has a wide range of adjustments to CPU settings, including CPU voltage and bus speeds.

Other Features
These days, most motherboards have a whole host of extra features loaded into them. These can include things such as on-board Ethernet, audio, a RAID controller or even graphics. I find such features very handy as they help you save money - you need not buy additional expansion cards.

Conclusion
In short, make sure you do your homework when purchasing a motherboard. Go to the motherboard manufacturer's website and read about its products. Download the motherboard manual and see if its well documented.

At the risk of sounding biased, I've always preferred ASUS motherboards. However, its all up to you. Consider what features are important to you and go get your motherboard. As I said earlier, don't scrimp on the motherboard. Its one of the most important PC components, so get the best you can afford.