Is it possible to enable "Focus follows Scrolling"?
I find that many applications already behave this way.  At least with a trackpad.

If I am working in this window, responding to your comment, and I hover over another Safari window, OR over my iTunes window, I can scroll without clicking on the other window.

My computer is not set to Focus follows mouse.

It may well be that some applications do not support this... 

Do you have a specific set of apps in mind?