For those that get here looking for how to change PWM frequency for the Due, you should look here for a solution: http://arduino.cc/forum/index.php/topic,131323.msg989728.html#msg989728
Basically, only pins 6-9 on the Due board are actual HWPWM and the other pins labeled as PWM are timer pins.
You can change the frequency of the PWM pins 6-9 with the following (changes the frequency for all the pins):
PWMC_ConfigureClocks(whatever_freq_you_want * 255 , 0, VARIANT_MCK)
I'm not sure how/if individual pin frequencies can be changed.
The same can be accomplished by changing #define PWM_FREQUENCY 1000 for the pins 6-9 and #define TC_FREQUENCY 1000 for the other PWM timer pins. These constants are defined in 'variant.h'.
Hope this helps someone along the road.