I have Fedora running on an older computer that I put an unused very-noisy HD in. The HD I removed from my "main" Win98 computer for the primary reason that it was so noisy. When Fedora is left on and it goes into "sleep" or whatever, the HD will start grinding away--doing ?something?, even when no applications are left running. What is the OS doing, and is there any way to make it not do this? Both computers sit right next to each other, so it is annoying to have to listen to and interrupt your work with the other computer to stop. If I go and open any program in Fedora, the HD searching halts after perhaps 5 seconds, but as soon as the PC goes to sleep again, it starts up same as before.
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Something's probably running on that machine. You probably forgot to turn on or more services off. Log in on the machine and run 'ps aux'. It'll show you al processes. If you don't know if all of them are needed, post the list to the forum.

Although this shouldn't be it, perhaps its your journal being written to. EXT3? ReiserFS?