This tutorial describes how to disable the pcspkr beeping - stops login screen beep (x1) and logout/shutdown/restart beeps (x2).
A. Stop the pcspkr module from loading:
In the Terminal (re)move /etc/modprobe.conf, if present, as it supersedes anything in /etc/modprobe.d/* (unless you add include/etc/modprobe.d).
In the Terminal create a file /etc/modprobe.d/pcspkr.conf containing: blacklist pcspkr
In the Terminal type: su
This gets you a login on the Terminal as root (you'll need to authenticate).
In the terminal type: depmod -ae
Ignore any warnings.
In the Terminal type: update-initramfs -u
In the Terminal type: exit
This puts you back at the Terminal prompt as the original user.
B. Configure Alsamixer:
In the Terminal type: alsamixer
Press [F5] to list all audio channels.
Look for a channel called 'Beep'. If there isn't one try selecting a different sound card by pressing [F6].
Once you have found 'Beep', highlight it and lower the volume to the bottom. Then press the [M] key on your keyboard to mute it. 'MM' should now have appeared in the square under the volume scale.
Press [ESC] to exit from Alsamixer.
In the Terminal save the Alsamixer changes by typing: sudo alsactl store (authenticating if neccessary).
C. Reboot:
Reboot the machine. If everything went well there will be no logout/shutdown/restart beeps heard or login screen beeps when the system comes back up.