Option to apply the mouse wheel to whichever window is under the mouse cursor
Additional comments:
(1) I believe this is already the case with MS Office 2013 programs (but not MS Office 2010 which I am using on the computer I am writing this on).
(2) If there is a slight delay after crossing a window border before mouse scroll will go into that window, consider showing this visually, for example a small rotating circle next to the arrow during the delay, or a change in colour of the window border when it becomes the receiver of mouse scroll.
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Lars Hallstrøm Eriksen commented
This is the same as a newer, better described suggestion with the snappier title '"AquaScroll" Feature', which has more votes. I have moved my votes there.