Kenneth needed to tame an old PC that was just too loud. He designed a fan controller based on the 16bit MSP430 microcontroller that adjusts the speed of 3 fans depending on the temperature of the CPU. Source code and schematics are available.
During the Maker Faire Salvage Crawl last month, I picked up a kiosk-size industrial computer for $20. All well and good, except that the BIOS in it made no effort to control the fan speeds, and instead simply ran all three cooling fans at full blast. This was unpleasantly loud, so I decided to simply build my own fan controller, using an MSP430, so I could easily monitor the system temperature and adjust the fan speeds accordingly.
You could have soldered your transistors (and the easily avoidable) 74xx14 on a little MSP430 LaunchPad ($4 shipping fees included). It would have costed less than the protoboard and all surrounding connectors :p
Another simple way to drop the noise level of the fans is to remove all the case baffles at the fan outlet. They’re just there for safety sake and if that’s not an issue, you can drop the noise level significantly.