The problem may be water lines that are not properly isolated from the structural elements of your home. If this is the case, the motion of water moving through the pipes may be transferring to beams, joists or studs in or beneath your flooring or in the walls. If the pipes are accessible the solution may be as simple as inserting an insulating material between the pipes and the structural elements they are touching. If your pipes only rattle when the water is turned on or off it may be that you need to install a water hammer arrester which will eliminate the jolt caused by quick closing water valves. This problem can be somewhat tricky to diagnose and you may want to consult a professional plumber.