Can you describe the sound better?
is it similar to the alert you get if you try to CMD+C (copy) something without anything selected?
There was a
Recent Thread about an unknown error sound.
I too have been hearing it for some time, but it didn't seem to be a huge problem, just an alert being caused by an unknown app. After reading the above thread, and realizing it wasn't just me, other people have been hearing it aswell, I decided to do an investigation.
Unfortunately, the problem appears to have resolved on it's own. With a pen and a pad to mark down the approx. time of each sound, I sat here for days without noticing any sound at all. To this day I still haven't heard it.
So much for my investigation...
Perhaps you can run it yourself.
Mark down the approx. time of each sound, and see if it truely is random, or if it happens in some type of pattern.
Check anything you can for the times you wrote down, console.app might have something.
do what you can to try and pin point it.