As others have already said, you absolutely have to have the right pin configuration on the motherboard to accomodate the CPU.
One that's done, then you have to consider both current and possible future use. Do you have a case that can accomodate only a micro-ATX board or can it take a full ATX or either one? Will you have a possible need for more than two (or three if it's triple channel) RAM slots? BTW, the RAM configuration (double or triple channel) will be determined by the CPU. How many hard and optical drives do you forsee using? Will any of them be IDE? Will you want to put hard drives in RAID configurations? Will you ever want to add a second or third video card? How many USB devices do you forsee using?
Those are just a few of the questions you need to ask yourself in order to select a board that will accomodate both your current and future needs.
The motherboard is a critical component of your system and it's selection should not be taken lightly. The motherboard, CPU and power supply are the pieces of your system that you're not likely to ever change out unless you've selected poorly.