NewWinMan

You can set the default action to nothing, activate, send to the bottom, maximize, minimize, restore, or close the window; and also has conditions to determine what to do with different groups of windows (up to 4) depending on their title. And this could be very useful for the management of pop-ups for example...

Besides all that, it can also order non-minimized windows in z-order (the order in which they appear when you press Alt-Tab), by title or by the order in which they were created. This will help you a lot to find an specific window if you have too many of them opened.