When your Mac 'beeps', check the Applications menu (aka process menu) in the top right hand corner of your screen - see if any applications listed have a diamond next to them. If so, they need your attention (error dialog most likely, except something like AIM which does that to show new messages
Does it by any chance happen every half/quarter hour? You may have your clock set to chime every so-often. Check your "Date and Time" control panel, under the "Clock Options" button (bottom right corner of the window. The aforementioned options are in the right-hand pane of the Clock Options window.