Comment 3 for bug 21584

(In reply to comment #2)
> (In reply to comment #1)
> > Thanks for your bugreport.
> >
> > This is really a limitation of the gnome-panel/gnome-menu system. To have it in
> > the root of the applications menu it needs to be included in gnome-menus, but it
> > also needs a "normal" location for other desktop enviroments.
> Thanxs. Then my suggestion is to remove it from the root of
> the applications menu.

Sorry, the decision to put it there was made by my boss Mark shuttleworth (sabdfl).

You can edit the file /etc/xdg/menus/applications.menu
and remove the:
<Include>
  <Filename>gnome-app-install.desktop</Filename>
</Include>

lines if you want to make it go away from the application menu.