Sometimes called "X Focus" or SloppyFocus, focus follows mouse is a different paradigm for selecting the active window in your WindowManager (or on your DesktopEnvironment).

With focus follows mouse, the active window (the window that will receive text if you type, for example), is defined not by which window is frontmost in the "Z Order" (Z being the third dimension, "into your monitor", in cartesian space), but by which window the mouse is over.

This is most useful for people who have multiple terminal windows open on their desktop. Unix hackers love it, everyone else finds it really confusing.

If you look at the BeOS Focus Follows Mouse example, you will get a good idea.

If you want this feature on MicrosoftWindows you can download the TweakUI powertoy and use the XMouse mode.