I don't know if the topic is still live or not but making an Arduino multi-channel fan controller has already been done, it gets the temp readings from the PC's on-board temp sensors.
The post covers 2,3 and 4 wire fans as well as the differences of how to use a 3.3v vs 5v Arduino for the controller. Even RGB programmable LEDS are supported as an addon option.
If anyone is interested the post can be found at http://www.silentpcreview.com/forums/viewtopic.php?f=9&t=65801&p=571959#p571959
If you would like more of a basic howto guide I posted one on my blog.