Auto Raise
This feature causes the application currently under the mouse point to become the front-most application, after a user-specified delay. It's possible to raise just the window under the mouse or all windows for an application.The feature is controlled by the 'Auto Raise' settings in the General Settings tab, which look like this:
In the screenshot above, any window under the mouse will be made the frontmost window after .20 seconds (200 milliseconds) of no mouse movement - but only when the shift key is held down too.
Try this out - it can be very useful, but watch that you don't set the delay to be too short - around 0.25s is probably the shortest time you want to set, otherwise your windows will almost instantly pop to the front all the time, which can be annoying.
Turning auto-raise off
To turn off auto-raise, simply deselect the 'Bring window under mouse to front after:' option.