Important Note

The PWM pin available on the GPIO header is shared with the Audio system. This means that you can't use PWM output and play audio through the 3.5mm jack at the same time.

Good resources

http://xoblo.gs/rpi/2012/09/01/pwm-driver-part-2:-research/

http://learn.adafruit.com/adafruit-raspberry-pi-educational-linux-distro/occidentalis-v0-dot-2