Same problem with a fresh install of Intrepid on an x60s.

The gconf editing solution from w1zard
(https://bugs.launchpad.net/ubuntu/+source/gnome-
session/+bug/290204/comments/12) does not work for me, but the
blacklisting solution of Vytas
(https://bugs.launchpad.net/ubuntu/+source/gnome-
session/+bug/290204/comments/7) does.

I didn't know how to blacklist, but there's an explanation at
http://ubuntuforums.org/showthread.php?t=166624 which boils down to
doing

sudo sh -c 'echo blacklist pcspkr > /etc/modprobe.d/blacklist-custom'

As the original poster mentioned, the Fast User Switch Applet doesn't
have the beeping problem, so just using that to shutdown, instead of
System -> Shut Down, is probably the easiest solution.

-- 
Annoying beep on shutdown using "System -> Shut down..."
https://bugs.launchpad.net/bugs/290204
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