Note: Klicko is no longer under development, and it is no longer available for sale.
Klicko... In the Classic days, if you wanted to use a window that wasn't frontmost, you could click anywhere on it to bring it to the front. Mac OS X introduced a feature called "click-through" where certain controls, like the "traffic-light" buttons in the window title, would work even for background windows. Applications can also make other controls, or even the entire window, work with click-through.
Klicko blocks click-through inside application windows. You can make a list of included or excluded applications, or hold down a modifier key to momentarily override Klicko.
Klicko is a System Preferences panel written in Cocoa. It doesn't hack the system, other applications, inject code or do anything magic. Klicko also has two other convenient functions: window maximizing and bringing all windows of some application to the front.