So I've always thought the perfect way to deal with window focus would be the following:

With two windows open (A and B), assuming A is above B, but B is visible behind A. (I.E. a terminal window on top of a web browser window).

Focus is initially on A (mouse and keyboard).
When the mouse hovers over B the scroll wheel is enabled for B, but keyboard focus is still in A. (So you can scroll a page on the web browser while still having the terminal on top.)

When the mouse is single clicked (or clicked and dragged, etc.) A is still raised, but keyboard focus goes to B. (So you can go to a different webpage without the Terminal disappearing behind the web browser. This would be great for copy/pasting things from one window to another).

When B is double clicked it is then raised and A is no longer in focus.

Does that make sense? I've heard that this isn't possible with the X server (at least without a LOT of hacking).

I'd like the ability to do highly customizable window focus (keyboard and mouse independent) like this.