Have you looked through the Interfacing With Software section of the Arduino Playground?
Also, while it would be possible to run the fans off the 5 VDC from the Arduino, it will be an extra current draw on the less than 0.5 A current limit of standard Arduino boards. If this is going to be interfacing with the computer, why not wire up an appropriate connector and run the fans, and perhaps the motors, from the computer's PSU?