My DH and I have both had the problem on our disc brakes, usually it is the rotor has been slightly knocked out of true. Pretty simple fix for the LBS but I don't attempt it myself. I have a thing about not working on my own brakes, they have too important of a job! The other thing I had was a problem with was non-organic brake pads, they were just noisy and I switched them out at the recommendation of my shop.