1. Make sure the motherboard has everything you need. Examples: SLI/CrossFire compatible, USB 3.0, enough SATA ports, enough RAM slots, mSATA, etc. Those are just examples. I'm not suggesting that you get a motherboard with all of the above. Also keep in mind the size of the motherboard. If you want a small computer and tower, then you'll want a smaller motherboard. And depending on your CPU, you'll also have to choose the motherboard with the correct socket as the CPU.
2. Popularity, reviews, benchmarks, etc.
3. ASRock, Asus, Gigabyte, MSI