If it is running fine then this will be something pretty simple like a key stuck down on the keyboard. It could also be a program or even a system warning.

Normally this is the keyboard that does it. If you put something on any keyboard after a bit you will get a continuous beep. So what you need to do is take anything off the keyboard (ok thats the obvious one) or look for stuck keys. Usually you see this from spills or dusty or oil environments. Flip the keyboard upside down and knock on it just like knocking on a door. Usually the keys that stick are on the outside edges or the larger or longer keys.

Sometimes a program will grab control of the speaker and generate the tone. This can be anything from a incoming fax o email to a virus warning. You need to check what is running and then if it is set to generate a tone. This is the biggest pain to do as you need to check all the setting for everything. You can cheat by killing off a program at a time. If the beeping stops then you know which one to reconfigure.

Third can be a hardware warning. If it were not working this would indicate a motherboard problem. since it is working then I would look at it being a overheating issue.You would need to check your fans and such for heat and dust build ups.

Those are the causes that I have run across and most of the time its been the stupid keyboard.