When looking for a motherboard, look for the features that it has, that will suit your needs. Like, does it have enough SATA or USB ports? Does it have more than one PCIe x16 slot, so I can Crossfire or SLI video cards? Stuff like that.
And also the chipset of the motherboard. If you're going Intel, P35, X38, or 790i. As they're the latest, and best right now. If you're going for AMD, look for 590 SLI or 790FX.
What sets one motherboard from another, is it's features. Top motherboards brands are, Gigabyte, ASUS, DFI, Abit, and MSI.