You can download hard drive S.M.A.R.T. software that can tweak the performance/noise level. Higher performance = higher noise level. I have done this on my hard drive to see what it was all about. The one I used was made by Hitachi and I have a Maxtor hard drive. At max performance you can here the drive pipping while it's seeking data. Take it down a notch, and sacrifice a bit of speed, and the drive becomes silent. You can find the "Feature Tool" here:
http://www.hitachigst.com/hdd/support/download.htm
You can also buy hard drive enclosures that fit in the 5 1/4 inch bay and help cool and quite the drive.
Another option is to buy some mass loaded vinyl and line your case with it to sound proof it.