Activate

Searching around the web, I got this nice feature for your Terminal: you can change focus between Terminal windows with simple mouse over window. Here is the command line :

defaults write com.apple.terminal FocusFollowsMouse -string YES

Of course, big screen Mac user has the advantage here because this feature only move the focus without moving active Terminal window.

Deactivate

To deactivate it, simply change the boolean value to NO.

defaults write com.apple.terminal FocusFollowsMouse -string NO