fancontrol

fancontrol is a shell script for use with lm_sensors. It reads its configuration from a file, then calculates fan speeds from temperatures and sets the corresponding PWM outputs to the computed values.

It has a couple of nice automagical config scripts that figure most of it out for you:

sensors-detect pwmconfig

Once set up, you can manually run fancontrol or set it up to run as a background service when the computer starts.