Brian Archibald :
Do you have any recommendations for a good fan controller? I have no idea if the headers allow voltage control, would I know by plugging in another fan to test it?
I'm using an NZXT Sentry Mix 2, and it's a pretty good product. It's compatible with 3 and 4-pin fans and is fairly robust with the amount of wattage it may handle.
Word from the wise, though, with hardware fan controllers. With no rhyme to reason, the fans themselves may make a weird buzz noise that, although not completely awful, is perceptible. One of my Enermax Magmas did this, while an Enermax Cluster fan had no issues. Very strange.
As for testing if the fan header on your motherboard can handle voltage, there are a couple ways to do this. One by looking in the BIOS and see if there is some sort of "cool n quiet" or "smart fan" feature - this should allow you set up parameters for your motherboard to automatically control the fans RPM, but only if they are attached to the motherboard. The second way is similar, but using a third-party program called Speedfan. Again, both of these methods will only worth with fans directly connected to the motherboard.