Make sure you read the X stuff on input focus! It is perfectly
reasonable for the user to be using focus-follows-mouse window manager
policy but for an application to shift the focus to another of its
windows (aka ^X-5-o should work). Then think about what the emacs
variable focus-follows-mouse is supposed to do.
My window manager policy is focus follows mouse (I hate click to
focus) and I have focus-follows-mouse set to nil -- it all works the
way it is supposed to. I remember much discussion about this a year
or two ago.
--pete