How to find out which program a default beep is coming from in Windows 7?

Download Microsoft/Sysinternals Process Monitor.

Start up Process Monitor and disable all of the logging except for File System Activity(all but one of the buttons on the far right part of the toolbar should be deselected). Now, clear the capture window (Edit -> Clear Display) and if you can force the noise to happen. If not, sit and wait until it does happen(you may want to clear every 30 seconds or so if it gets too noisy).

After you hear the noise, stop capturing(File -> Capture Events), and search(Edit -> Find) for .wav. Locate any reference to the default beep sound file. That should lead you the process that accessed the file and caused the sound.

Have you tried to look at the mixer? It displays each program that is outputting sound and a volume control with a bar showing sound level output. Click the speaker by the clock then click mixer. Watch for the bar to spike when the sound happens.