Well start by what I said, get an appropriate PWM fan, an arduino and a temperature sensor. And it sounds like you have the temperature sensor picked out.
Have you chosen out fans?
If not check http://www.digikey.com or any of the other electronics distributors. Figure out what kind of size you need, and how much airflow. Make sure it has a PWM input, that way you don't have to include complicated extra hardware. As for air flow, what are you trying to cool?