on ubuntu 12.04 with gnome-shell:
with your notification sound "mybeep.ogg", stereo file, possibly WAV (or .ogg) and with a sample rate of 44100 Hz:
sudo mv mybeep.ogg /usr/share/sounds/
sudo gedit /usr/share/gnome-control-center/sounds/gnome-sounds-default.xml
add an entry just before the last line (which is
<sound deleted="false"> <name>My own beep</name> <filename>/usr/share/sounds/mybeep.ogg</filename> </sound>
All that’s left is to open Preferences > Sound (or gnome-volume-control at the command line) and select the new entry in the list of possible alert sounds.