In Ubuntu Jaunty final beta (I haven't tried with the release candidate yet, and this mostly didn't happen in Intrepid; see below), there are several system beeps when I shut down the system. The number seems random, generally at least 4 and sometimes as many as about 10 (it's hard to count, they often come rapidly); this is particularly annoying due to other bugs such as bug 335189 and bug 301174, but seems to be a separate issue; the problem isn't what the beeps sound like, but because they're happening at all. I'd expect a shutdown to cause no system beeps (and possibly a customizable shutdown sound).
The problem seems to be that shutdown(1), or something that looks very similar based on its effect on a text terminal, is being run multiple times at shutdown for no apparent reason; shutdown(1) emits a single beep when run to cause a shutdown (as a method of alerting people on text-based terminals), and so running it multiple times causes multiple beeps. I'm not sure why it's run multiple times, though (once would be enough to halt the system), or why going via such a noisy program is needed at all.
In Ubuntu Intrepid, this problem only ever came up at shutdown when I had previously been logged in on one of the text terminals (such as via Ctrl-Alt-F1), in addition to the graphical terminal; arguably it's expected behaviour in that circumstance (although the beep sometimes started at the shutdown and didn't stop until the system had finished shutting down, which definitely isn't). However, in Jaunty it also seems to happen if I've done nothing except via the graphical login since the computer was rebooted.
I'm not sure which package the bug's in; gdm seems possible, but it might also quite possibly be somewhere else. (It may be worth comparing a Kubuntu install to see what happens there.)
If there's any more information that would help, please let me know; unfortunately, I'm a little vague on what's causing this, so the bug report is a little vague on the details.
I've got the same bug. But for me there was always one beep at shutdown on Intrepid. I thought it was normal because of the shutdown command, wasn't it?
Now, on Jaunty, it's like 4 beeps in a row... It seems a bit random, but always in this range.
I agree with you for the whole system beep at shutdown. It'd be better to not have any when we're in graphical mode (and why not a nice shutdown sound if some wants it). And if the shutdown is asked from command-line, then maybe a beep if necessary (if it was just for me, I'd disable this one too... It's such an annoying sound!).
FYI, I installed Intrepid from scratch and, later, updated to Jaunty.