If it's a sharp shudder in the pedal, it's so-called warped rotors. Rotors don't actually warp, but they can wear unevenly so the thickness isn't uniform. Once it starts, it gets worse with use.

It's been maybe five years since I had a set turned and I don't remember what the machine shop charged, but it's not teribly expensive -- maybe $40 to do both if you bring them in loose from the car.