Comment 18 for bug 414795

pcspkr is now blacklisted. That is the expected behavior. However un-blacklisting it, and loading the module, should result in the sound being played again. However if i understand bug #77010 Pulse Audio is supposed to now take over and play a user defined, and much more reasonable, beep.
In the above referenced bug there are a few ways mentioned to turn off/on this beep including gconf-editor. I am not sure if this might help you Ahmed get your beep back.