On MacOS X, the default focus model is click-to-focus, presumably for hysterical raisins. There is not even a real choice. While tools like MondoMouse come with an option to enable a focus-follows-mouse policy, I found it does not work too well. Many OS X applications started behaving strangely.
However, at least Apple's Terminal.app can be changed to behave sensibly with respect to focus-follows-mouse. This hopefully prevents most instances of keyboard input going to the wrong window. To activate:
defaults write com.apple.Terminal FocusFollowsMouse -string YES
defaults write com.apple.Terminal FocusFollowsMouse -string NO
Some time after I wrote this entry, Tom Harrington emailed me, and asked what snags I encountered in MondoMouse. I could not tell him specifics any more, as the 30-day trial period had expired by then. Very kindly, he provided me with a complimentary licence, so that I could try it out again. Kudos to him!
Now, a year onwards, I am happy (and heavy!) user of MondoMouse, namely its window moving and resizing features. As time progressed, I have not felt a need anymore for the Focus-Follows-Mouse feature. It might have improved by now.