For a couple of weeks my MacBook Pro had made intermittant, seemingly random, beeping sounds and I couldn’t figure out what program or process was caussing this behavior. It was driving me nuts!

after a lot of googling the solution in the end was pretty simple.
Here’s what I did:

There is a program called opensnoop installed on Macs that tracks file openings.
And since it was likely that a sound file (with the aiff extension) was opened to play the sound I typed this into a terminal:

$ sudo opensnoop -v 2>/dev/null | grep "aiff"

and waited. The next time the sound occured it printed out the process that caused it.
Turned out it was some misconfiguration in the OS X notification center.
I turned that off and the problem was solved.