If you've disconnected the system speakers and you still get a noise(beeps), then you have a "vibration" or resonance sound. A fan when going out can do this as it spurts along in stop&go operation, check all fans to include the power supply. A loosen screw on some area is vibrating or gone(dropped) and the loosen device, clamp, plate, whatever has enough force to vibrate. Last, a modem card with mounted speaker can cause feedback due to degraded condition and RFI(interference) gets routed thru the speaker. The movement of the mouse can cause this as well. If modem, remount in another slot or replace. -OR- try another mouse. All of this maybe the result of a 5yr. old system that starting to degrade enough for flaky or weird problems if anything, annoyance. Look into all that plus what other posters suggested. A good cleaning and then inspection is always in order.
tada -----Willy 