macegr: I'm afraid that the frequencies in your post for pins 3, 9, 10 and 11 are a little of. The correct formula is f = clock/(510 N), where N is the divisor (prescaler) and clock = 16,000,000. That gives f = 490.196 Hz for the default setting. But close enough. See the ATmega168 datasheet.
westfw: The reason is that Timer0 runs in the FastPWM mode to feed the millis() function. That gives a frequency f = clock / (256 N), N = 64 by default. In FastPWM, the counter is always incrementing until it reaches 256 when it overflows to 0. The frequency f = 976.563 that is close enough to generate milliseconds.
Timers 1 and 2 run in the Phase correct PWM, which is apperently better for motors. Then the counter increments until it reaches the top 255 and then starts decrementing until it reaches 0. And then again incrementing... Thus for each cycle it has to go through 255 + 255 = 510 steps, hence the frequency clock/ (510 N), N = 64. That gives you ~~ 490Hz.