Macbook Air 2012 single beep while on
SoundBunny has a free demo available which will work for 30 days, this app will show you every app which is makes a sound. That might help you track it down. You can also tell it to ignore apps which you have ruled out, which should help you narrow things down a but too. The purpose of SoundBunny is to let you set the volume for each app, but I thought it might help with this as well.

TJ Luoma posted this answer to a similar question here: apple.stackexchange.com.