By default, mouse focus for Terminal is determined by clicking on the desired window, but it is often more convenient to have the focus automatically follow the mouse to any Terminal window.
defaults write com.apple.terminal FocusFollowsMouse -string true
To make the command take effect, you need to restart Terminal.
Revert to the default setting, change boolean in false
defaults write com.apple.terminal FocusFollowsMouse -string false
Does not work under 10.8
Here no problems 10.8.3
Works great for me. Tiago did you quite and restart Terminal?