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Fan Controller Software

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There's Speedfan, but I don't know of any software that actually works well. A hardware controller is cheap and much less headache.

ASUS also has Fan Xpert or something if you have an ASUS board.

GPU fan, use MSI Afterburner, that does work well.
 
^pretty much sums it up. For the kind of control you're probably looking for, a physical fan controller is really the only way to go.
 
Link me to one Ehume

Basically any Gigabyte board. Their ET6 software looks pretty basic -- no glitz -- but it has all the function you need. Or you can do some work in their BIOS. Their newest BIOS has a number of variations you can use, some that require actually . . . reading the manual (shock!).
 
I dont know of any good software controllers, but my sentry 2 is awesome for controlling fans. You can also get really cheap plastic ones off of newegg for 5 bucks.
 
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