
Microchip describes techniques to reduce acoustic noise in pulse width modulator controlled fans. One solution is to use an RC filter to decrease the slew-rate of the PWM pulses.
Fan speed control extends fan service life and decreases airflow noise and average fan current. The most efficient way to implement fan speed control is to use low frequency pulse width modulation (PWM). However, PWM fan speed control can sometimes introduce unwanted acoustic noise at a frequency equal to that of the PWM itself. This is especially noticeable when PWM control is used with higher operating current (>300 mA) fans and at low operating speeds. This application note discusses the source of this acoustic noise and a method to suppress it.

As someone who works for a fan manufacture and a developer for controllers I’d like to say this:
PWM control of fans like this can atually reduce fan life due to the high switching current. Microchip are correct that these steps will help this and help reduce noise, however…
There are a number of PWM (four wire fans) designed to work with a PWM input. You dont have to switch the power on and off, there are quite and have long lifes. Useing a cheap fan and adding speed control like this only risks your eqipment you are cooling, from over heating when a fan fails.
If you realy want to keep your two wire fan, then look for controllers that are designed to control them, ones that dont PWM speed control them.
If people what to know how to do this, please contact me on twitter via @monpjc where I’ll be happy to help developers.
Thanks
Paul