Damping your HD is the best way to isolate the noise. ( assume you did omit the fan noise as previous posts )
I use the following stuff in my PC.....
However, the suspension kit is not cheap...... Finally I found a way and it is free. ( OK, almost free ) You use wire ( or your shoe lace and tie your HD in the 5 1/4 DVD driver bay. The key is to make sure there is no metal contact to your case. You will find how quiet it is. You should be careful when you move your PC if you are doing this.
