First, you need some cpu temperature monitor software. For Ubuntu you need to install a package called lm-sensors. It's available in Ubuntu's main repository. All the commands listed in this howto should be executed from the terminal.
Then you need to run sensors-detect.
and just follow the prompts. Add the recommended lines to /etc/modules.
Now, if you don't want to reboot, you'll have to manually activate the modules.
where module1 etc. = the module names provided from sensors-detect.
Next, you need to create your fancontrol file. The easiest way is to run pwmconfig.
and work your way through the instructions there.
Finally, run sensors -s to make your fan configuration take effect.
Now, you can check your temps.
Now to run fan control, type:
To have fancontrol run on startup, follow the instructions on the Ubuntu Forums. Note: This step is no longer required in 9.10 Karmic Koala. The fancontrol script is already included in the build. It will start automatically the next time you boot.
To monitor temps and speeds, I like gkrellm. To get it:
Here's a screenshot of Gkrellm.