I get a clunk noise when stepping on and releasing the brakes occasionally but not always. This occurs even with the engine off and the vehicle stationary. I also hear some other noise like some sort of vacuum servo thing is happening.
Check out my thread, I think we have the same issue: http://priuschat.com/forums/gen-ii-...und-when-shifting-using-brake-video-link.html
My 2006 with 125k started making a clunk sound which could be felt under your feet when first applying the brake. It almost felt like a rod on a cam releases when you touch the pedal and it contacts something with a "clunk". It seems like it started immediately after a panic stop where I really mashed the pedal. The clunk also seems random and doesn't happen every time the brake is applied but it happens 80% of the time and 99% the first time after the car is started. The car now has 128k miles on it with no service in between the time the clunk started, and for the last 500-1000 miles, the clunk has disappeared.