i had the same problem, and by turning on the tap in the bathroom sink whilst the toilet is filling solved the problem. having read other fixes on the net, it seems as though it is too much pressure filling the cistern causing the ballcock to bounce about shutting the filler valve on and off. this in turn causes greater pressure back down the pipes making them vibrate loudly. So all i did was to slightly close the shut off valve inline just before the cister. by tweaking how much i closed this valve completely cured the problem. this will probably only be a temporary fix i suspect the whole ballcock and inlet valve will need replacing at some point soon, but hey no more noise :)
dave kendrick, March 2011