I find picking motherboards comes down to the real basics. Does it have the inputs and outputs you require? Does it have the required number of USB 3.0 ports at the back and mid to supply the case ports? Does it have the number of SATA ports you want? eSATA? Does it have the PCIe slots you need? Does it have the number of fan PWM connectors you need?
That said I'm a bit partial to Asus for their FanExpert fan control system. I like to be able to customize the way the fans run so my PC is quiet. Getting a quiet PC is kind of counter intuitive. If you select a high capacity cooler with big fans, you can often run it and the case fans at minimum speed 95% of the time, and have it almost dead quiet.