For example, to disable <F1> shortcut in Gnome Terminal (in order to pass it to, say Vim), do the following:

  1. Go to System > Preferences > Apperance, Interface tab, make sure that ‘Editable meny shortcut keys’ enabled.
  2. In application window, Gnome Terminal in our example, click Help > highlight ‘Content’ and press ‘backspace’. The key designation after the ‘Content’ will disappear. You can re-assign a key later by doing the same, except for pressing a key other than ‘backspace’.

Taken from here:

http://linux.derkeiler.com/Mailing-Lists/GNOME/2007-03/msg00010.html