So, I was was getting irritated by a faint beep that sounded like it was from the motherboard. I hit Google and it looked like bad news - dead hard drive. I backed it up, and started going through my warrenty info, but I just didn't see the performance drop you usually get with a bad drive.
I found a few posts that mentioned that some updates can mess up the speaker. They recommended updating the machine. I had Leopard and just hadn't gotten around to loading it. I loaded it - it was a very easy upgrade. The beep was still there. I then chose software update from the Apple menu and after those updates were applied, the beep was gone.
So, if you have a strange beep, first back everything up and then update. If it still beeps, take it in for service.