Fluctuations in activity and not actually turning on/off? The hard drive is usually quite, so you typically won't hear it unless it's under a high level of activity, heavily fragmented, or damaged. A few things you could check the next time it happens include:
1.) Open My Computer and see if the drives are still listed/accessible.
2.) Use a hard drive monitor such as Steller Smart to keep an eye on it.
3.) Leave your case open, touch the metal frame a couple times, then feel the hard drive(s) to feel if they're still spinning.
4.) Check the S.M.A.R.T. results with a tool such as DiskCheckup.
5.) Run chkdsk, the Windows tool/command, on all of your drives.

If a hard drive is actually turning itself off, it could be detrimental. Obviously data loss is a possibility should it turn off in the middle of writing, and if it's a power problem it could do physical damage. Thus, it's definitely worth looking into, just in case.

John