I really don't understand why you guys are not fully using the the complete potential of timer possibilities, of course requires fine register initialization but you could get very precise high frequency PWM even beyond 500 KHz or 1 MHz.
For the moment, i've doing so for years with arduino mega on my power electronics project (plasma drivers, full H-bridge, MWO inverters...) many of them, see old post then specific update code even though now is even more refined http://arduino.cc/forum/index.php/topic,8162.msg65115.html#msg65115 )
I do have an arduino DUE but as explained on other threads recently, I cannot download my actual MEGA projects using advanced arduino mega timer management because USB link of DUE is full of bugs.
Again I insist, just program the proper WAVESEL value and other registers, there is NO need to make interrupts slowing down and skewing the PWM jitter precision if using a timer, in particular with DUE being much more sophisticated timer possibilities than MEGA !
Just my 2 cents