Extraneous noises really bother me. No, I mean really.

basic beep

X Window /etc/X11/xinit/xinitrc xset b off
Gnome 3
Settings > Sound > Sound Effects > Alert volume ⇒ mute
or /desktop/gnome/sound/event_sounds=false in gconftool
terminal emulator varies
Most terminal emulators have a way to stop the bell.
GNU Screen ~/.screenrc bell_msg "" # don't change the message-line whenever a bell occurs vbell off # don't react to bells visually -- rather, pass them on unfiltered to the real terminal
Bash ~/.bash_profile setterm -blength 0
Bash/et al ~/.inputrc
/etc/inputrc
set bell-style none
Vim ~/.vimrc set noerrorbells " this one may fixes most beeps, you may only want this one. But if you want complete silence, inlude the other two set visualbell set t_vb=

other noises

Ubuntu 10.10
System > Preferences > Sound > Sound theme ⇒ No sounds
System > Preferences > Startup Applications > disable GNOME Login Sound
System > Administration > Login Screen > disable Play login sound
sudo mv /usr/share/sounds/ubuntu /usr/share/sounds/ubuntu.disabled