Originally Posted by c0rr0sive
... Could also be the hard drive failing.
I thought that at first too, but OP said this had been going on for a year or so. Don't think a hard drive can be in the 'failing' stage for a year without causing at least
intermittent issues, and since a cleaning didn't do it, I'd put my money on a non-essential hardware failure, since you can still use the PC without issue (aside from the annoying sound).
Try unplugging the CD drive from the power supply and booting it up. See if you still hear the sound.