When it comes to brakes, there are no good vibrations. The most likely reason that you feel vibrations through the brake pedal is because a rotor — the rotating disc that the brake pads are pressed against — is unevenly worn, or what some call "warped." (It's unlikely that a rotor could truly warp from normal use as opposed to a manufacturing defect, but thinner and thicker sections — uneven wear — have the same effect.)
Brake vibration, or what some refer to as a shudder or pulsation, often is the result of parts of the rotor being thinner than others instead of uniform all around. As the brakes are applied, the pads will be pressed against high and low spots that the driver feels through the pedal. Rust and dirt also can build up on a rotor and cause minor pulsations.
A rotor's thickness needs to vary by only a few thousandths of an inch for the driver to feel it. In more serious cases, the whole car can shake when the driver hits the brakes.
One cause of distorted rotors is that the brake pads, the friction material that gets pressed against the rotors, aren't being fully released when you remove your foot from the pedal. If the pads "drag" on the rotors too long, the rotor and/or the pads can become damaged.