You can get HD cradles that fix your HD onto rubber support to cut down on sound. (
http://www.dansdata.com/novibes.htm )
they use the 5 1/4" bays though so you may not have the room.
I know what you mean though with the sound... all my noise comes from my PSU fans (soon to be fixed with a couple of resistors to bring them down to 7v) and my Hard Drives.
Next time I'll try and get one of those silent drives and use a file server for all the rest of my data... in another room.