Here is a patch (against CVS HEAD) that adds XEmbed support for all X
flavours and makes keyboard focus work for the GTK version.  It needs
the gtkplug, parentid and parent-fix patches [1].

[1] http://lists.gnu.org/archive/html/emacs-devel/2005-12/msg01558.html

Some issues:

* The current implementation is minimal although all XEmbed message
  types and parameters are enumerated in src/xterm.h.  It is not clear
  to me if the additional protocol features are feasible for Emacs or
  how to implement them.

* Emacs requests focus only when the buffer area is clicked.  It might
  be a good idea to request focus also when the menubar or the toolbar
  is clicked.

* I'm not sure if src/xterm.h and src/xterm.c are the correct files for
  the XEmbed enums and utility functions.

* The implementation of XEMBED_FOCUS_{IN,OUT} seems clumsy.

* I tested only --with-x and --with-gtk configurations.

* The keyboard focus works correctly (at least) under Metacity, but
  there seems to be a problem when using the Ion 3 window manager.  The
  original GtkPlug version could only be used with Ion because it seems
  to treat embedded windows like top-levels as far as focus is
  concerned; the embedder application is not in charge.

timo