All fans in my desktop PC are 120mm ones, all are temp-controlled and running very slow on low load/temps. Additionally I replaced the 120mm inside the PSU with a slower running one. The CPU is cooled by a big ass tower-cooler that also helps to maintain a good airflow to the upper rear of the chassis.
Use this on Windows PC to have fanspeed controlled by software depending on temps. You can customize temps for low running and high running fanspeeds as much as a critical temp where the fan will run at 100%. Your board has to support controllable fanspeeds though.
SpeedFan - Access temperature sensor in your computer
In order to keep my harddrives quiet I placed them on foam and did not screw them to the chassis in order to keep the chassis from resonating the HD's vibrations. When idle/under low to medium load the HD can still be heard on random access, but not its motor-spinning. I'm one of those guys who actually even prefer hearing the HD do its work as long as the motor keeps quiet.
This is the chassis I'm using. I removed the front aluminium shield for aestetic reasons and closed all side openings in order to improve airflow from lower front to upper rear.
PCI Case Germany GmbH
Except for the HD access the PC noise is below ambience in my rather quiet room. Heck, that damn TFT display's background light is humming louder when I lower the brightness.