You can disable this by editing a file and entering two simple lines.
gedit /etc/modprobe.d/blacklist
And then add:
#silly speaker beep
blacklist pcspkr
Save your file and the speaker beep will be gone when you reboot.
If you don’t want to wait until a reboot, simply type:
sudo rmmod pcspkr
Original post: http://www.arsgeek.com/2006/08/23/how-to-turn-off-the-annoying-system-beep-in-linux-debianubuntu/