The system beep on my computer is way too loud and is really annoying. To permanently disable it, type the following in the terminal:
echo “blacklist pcspkr” | sudo tee -a /etc/modprobe.d/blacklist
To put it into effect, type the following in the terminal:
sudo modprobe -r pcspkr
When you log off you should no longer hear the beep. It works at least on Ubuntu 9.04.