The best solution we found was "hdparm -Y /dev/hdX" (and /dev/cdrom). 
It works on hard disks if not all CD-ROMs.

The other noise is the power supply fan.  Stock PCs offer no s/w fan
control.  Some PowerPC machines have it (although Ubuntu-PPC/Debian-PPC
still has serious bugs).

http://www.silentpcreview.com
http://www.endpcnoise.com

Mark
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