I don't know what metacity is supposed to do about this. Does it work
with any other window manager? How?

It works with CDE's dtwm. It returns focus to
the application as soon as the Atok12 window is 
unmapped. 

In general, this is controlled by autoKeyfocus
settings, written below. It is True by default.

       autoKeyFocus (class AutoKeyFocus)
                       This resource is available only when the
                       keyboard input focus policy is explicit.
                       If autoKeyFocus is given a value of True,
                       then when a window with the keyboard input
                       focus is withdrawn from window management
                       or is iconified, the focus is set to the
                       previous window that had the focus.  If
                       the value given is False, there is no
                       automatic setting of the keyboard input
                       focus. It is recommended that both
                       autoKeyFocus and startupKeyFocus be True
                       to work with tear off menus.  The default
                       value is True.

FYU, startupKeyFocus is defined as below.
I think metacity behaves samely at the moment:

       startupKeyFocus (class StartupKeyFocus)
                       This resource is available only when the
                       keyboard input focus policy is explicit.
                       When given the default value of True, a
                       window gets the keyboard input focus when
                       the window is mapped (that is, initially
                       managed by the window manager).  It is
                       recommended that both autoKeyFocus and
                       startupKeyFocus be True to work with tear
                       off menus.  The default value is True.

I guess metacity is already supposed to do that (focus the topmost
window when the current focus window closes). I'm not sure why it
isn't happening.

Metacity on Solaris returns focus to the topmost when gnome apps(I
tested with gnome-terminal and gedit) closed. When non-gnome apps such
as xterm and CDE dtterm closed, it returns the focus to input method's
status window attached to the 
topmost window.

I'll attach a screen shot.
 A small window leveled "ATOK" gets focus when  
 xterm or CDE closed. The "ATOK" is a tranient   
 child of the terminal window.
 (It does not look like taking focus, since I
  had to move focus to hit screen_shot button..)

And when Atok12 lookup choice window closed,
it however does not return focus to either the
topmost or the status window - no window has
focus. Any insight?

Created attachment 11499 [details]
ATOK status window gets focus when the app closed

Not obvious to me what's wrong. You might try looking at the 
log file or attaching it here. 

(Run a new metacity with METACITY_VERBOSE=1 METACITY_USE_LOGFILE=1 -
you could do it with "metacity --replace" to replace current metacity.
Quickly reproduce the bug, without doing anything else to clutter the
log file. Then pack up the log file and attach to the bug report, 
or "grep FOCUS" in the logfile and look to see what goes wrong.)

Created attachment 11501 [details]
log file - open ATOK candidate selection window once and close

I attached the whole log. When a gnome-terminal 
is served by Atok12 input method, I run a new
metacity, and bring up Atok12's choice window 
and close it.

Havoc, how about adding window->take_focus check
to get a default_focus_window in window stack?
A patch will be like below. This has fixed
a problem for me with Atok12's candidate window.

Index: stack.c
===================================================================
RCS file: /sgnome/cvsroots/sun-gnome/metacity/src/stack.c,v
retrieving revision 1.3
diff -u -p -r1.3 stack.c
--- stack.c	5 Nov 2002 18:15:54 -0000	1.3
+++ stack.c	12 Nov 2002 21:08:58 -0000
@@ -1307,7 +1307,8 @@ meta_stack_get_default_focus_window (Met
            * focusing dock, even though docks are stacked higher.
            */
           if (topmost_overall == NULL &&
-		window->type != META_WINDOW_DOCK)
+		window->type != META_WINDOW_DOCK &&
+		window->take_focus)
             topmost_overall = window;

           /* We could try to bail out early here for efficiency in

It should be (window->input || window->take_focus)

Otherwise yes that seems sane.

Thanks, will you please commit this to the HEAD?

Yes, done.