Two suggestions...
1. Clean the dust out with a can of compressed air. This might help with a lot of the noise.
2. You say this happens when you leave your computer idling...it could be auto-defragging. This happens sometimes when I let my computer idle and it can be quite noisy. If you are using XP, then download
TweakUI. Then click on General, scroll down and uncheck
Optimize hard disk while idle, and click OK.
Leave your computer idle again and see if these suggestions work.