Yeah, large transparent windows, especially stacked, will tend to slow down your machine. It has to do two multiplies and a divide per pixel for each transparent window, that will seriously suck if you don't have hardware acceleration, and may be slow even with it. Normally Windows doesn't even paint the windows underneath, so there's a huge difference.

RabidVWM's ^@ch^ is fairly close to "active windows' handle", though probably not perfect. All other windows are inactive.