Comment 5 for bug 1103660

Which apps are displayed is governed by etc/xdg/pantheon-applications.menu, which is installed by slingshot. You can get ibus-setup to appear by explicitly including it in e.g. the System Tools section of this file:

  <!-- System Tools-->
  <Menu>
    <Name>System</Name>
    <Directory>System-Tools.directory</Directory>
    <Include>
      <And>
        <Or>
          <Category>System</Category>
          <Category>Administration</Category>
        </Or>
        <Not>
          <Category>Game</Category>
          <Category>X-GNOME-Settings-Panel</Category>
          <Filename>debian-xterm.desktop</Filename>
          <Filename>debian-uxterm.desktop</Filename>
          <Filename>ibus.desktop</Filename>
        </Not>
      </And>
      <Filename>ibus-setup.desktop</Filename>
      <Filename>ubuntuone-installer.desktop</Filename>
      <Filename>ubuntu-tweak.desktop</Filename>
    </Include>
  </Menu> <!-- End System Tools -->

Or by adding the category "System" or "Administration" to ibus-setup.desktop

It would also be possible to add the Category "Settings" to the System Tools section of pantheon-application.menu, but this increases the number of applications appearing in this section significantly.