I am aware that this is a rather old thread, but as this question is still relevant and on the top of many peoples minds and the (imho) best solution was not even mentioned, I thought I would add this one here as reference in case someone else is searching for a solution and was stumbling on this thread just as I had before.
To control the case fans based on temperature of your GPU (or a combination of GPU and CPU or even disk temperatures or temperature readings of sensors on your motherboard) you should give Argus Monitor a try.
When it comes to fan control, there is at the moment nothing that comes close in the usability department. It's easy to configure (unlike SpeedFan where you have to watch or read some tutorials to figure out how to configure it), but the GUI looks rather dated (some might say 'retro' ;) ).
The only downside is that it's not completely free (but the price for the license is very low, so for me this was no real 'downside').
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