Binary package hint: gnome-session
gnome-session-properties should filter by the NoDisplay key[1]. For all the same reasons it makes sense in menus, it makes sense for autostart.
With NoDisplay, one can install programs that run when the user logs in, but that the user should not be allowed to disable easily. Things that would break their setup if they disabled or just don't make sense to disable.
As an example, I (in Ubuntu Intrepid) have both 'xdg-user-dirs-gtk-update' and '/usr/bin/canberra-gtk-play --id="desktop-login" --description="GNOME Login"' in my list. Both should probably always run or have other ways of being controlled. As a user, I don't really desire to control whether they are autostarted or not. They are 'system-level' autostarts.
There is a patch in the upstream bug.
[1] http://standards.freedesktop.org/desktop-entry-spec/latest/ar01s05.html#key-nodisplay
Would be nice to get in lucid, could you add a debdiff to the bug and subscribe the sponsors so it stays on the list of changes to review there too