When any valve is turned off suddenly, there exists an effect called "water hammer".
Water hammer occurs because the momentum of the moving water in the pipe has no where to go when the valb=ve is turned off. Thus, the momentum of the water moves inertially towrds the end of the pipe, or valve, and then slams against it, recoils and then does it again and again until the energy dissipates . The higher the pressure or volume of water, as well as the more suddenly the valve is closed, causes a more violent water hammer. Some homes are plumbed with T's and a vertical extension of the pipe right before the pipe exits the wall to the fixture that it supplies. Thus when the valve, or fixture is turned off, the water coming through the pipe has a place to go (up the extension in the wall) rather then slamming against the valve. This also dissipates the energy without rattling the pipes.
Toilet flush valves, by their nature, tend to turn off the water very suddenly as the float valve reaches its level and shuts off almost instantly (as opposed to a slowly handle turning on a sink or shower). IT IS possible that the noise and rattle has gotten worse because someome has either turned the valve supplying the toilet all the way up, or higher then it was before. Its also possible that the water hammer has finally "shaken" loose the holdown clamps or pipe straps that hold the pipe to the studs inside the wall, and that they are now so loose that there is more motion of the pipe, and thus more momentum of the pipe as it rattles in the wall.
Water hammer can be a VERY powerful force. A freind of mine was upgrading a small townships water lines and pumps to a new storage tank up the mountain a ways. When he turned on the new valves he spotted a small leak (small, that is for a 6" main) and turned off the new valve. Well, the force of all the inrushing water stopped when it hit the closed valve, and literally blew the pump right before it 30' into the air, cause it wasn't strapped down yet! Needless to say, the pump was destroyed when it hit the ground again. It was an expensive and potentially dangerous mistake on his part. The water hammer that you are experiencing is, of course, a much less intense force.
If you don't mind a slow filling toilet, try turning down the valve which supplies the toilet WAY down, so the toilet fills more slowly. That SHOULD make the water hammer effect less powerful, and thus the pipe rattle less intense. Good Luck.