Why not do temp controled PWM?

You could nail the fan with constant 12v for a second (or less) and then use PWM to keep it rotational speed way way down. Ramp it up if the temp goes up.

There are single chip (and near single chip) PWM fan controllers.

This should be able to turn the fan slower than simply lowering it's input voltage. Plus you aren't wasting power (not like with a resistor anyways).

Could do it with a simple micro and jack it into the serial port. Then you could have a userland app or hijack mod which would allow you to control ramp up, thresholds, etc.

I was going to look into it more in my copious amounts of free time. At the least a fan controller IC should be a good option.

-Geoff