One thing that I found to be important, when choosing a motherboard, is the number of internal USB headers. There are a number of things that can be attached this way, such as:
Remote Control Receiver (internal)
Front USB Port(s)
Front Memory Card Readers
I'm sure that I'm forgetting some, but that would be three, and most mobo's only have two. Some only have one.
The reason this stood out for me, was because I have a case where the MCE remote receiver is mounted internally. I had to route the connection out the back, and plug it into an external USB slot. I know that the MCE receiver has a USB plug on the end, but I'm sure that I could have modified it.
Here is the case that I ran into that situation with. See all of the front ports that need a connection, and let's not forget the MCE receiver.
http://www.newegg.com/Product/Produc...82E16811128022