The recent push for the Unity desktop manager for Ubuntu, Debian...has prodded me to try it out.
One of my first challenges was enabling the focus to follow the mouse location. No simple way to do it via preferences, however:
$ gconftool-2 --type string --set /apps/metacity/general/focus_mode mouse
$ gconftool-2 --set /apps/metacity/general/auto_raise -t boolean false
That'll do it.