On my home server which I built on an old laptop the hard drive constantly made some noises. Sad thing it's the hard drive head's parking noise. Debian parks the heads every few seconds. smartmon-tools shows, the hard drive was almost at the death door. To tell the hdparm turn off the aggressive power saving behaviour, using the following command: hdparm -B 254 /dev/hda
The noise has ceased. But I still don't know why the system access the HD so often.