To turn off the beep in several applications:
For bash and other readline applications, create a new file $HOME/.inputrc and put the following line in it:
set bell-style visible
This can also be done system-wide in /etc/inputrc.
For gnome-terminal, go to the menubar Edit -> Current Profile. In the tab General, remove the check before the option Terminal bell. Click Close.
For Firefox, go to about:config, search for option accessibility.typeaheadfind.enablesound and set it to false.
For Thunderbird, go to menu Edit, Preferences, General and remove the check from the "Play a Sound" option.
For less, put the following line in your $HOME/.bashrc:
export LESS="-Q"
For vi, put the following line in your $HOME/.vimrc:
set visualbell
Some GTK apps, such as Pidgin and XChat, beep when you make an error during input (example: press backspace in an empty input field). To disable this, put the following line in your $HOME/.gtkrc-2.0 or $HOME/.gtkrc.mine:
gtk-error-bell = 0