How do I make OS X auto focus on the window in the screen the mouse moves into?
I made a python script that does this. Check it out:
https://bitbucket.org/sivann/mac-screenfocus/src

It focuses the last app that had the focus before the mouse left the screen. No mouse clicks happen behind the scene :-)

In my setup, the external monitor is on the left, it may not work in the reverse, let me know..