Mac OS X: If you have a billion windows open right now, all vying for your attention, HazeOver will help you stay focused by making them transparent, helping you focus only on the active window.
While it isn't for everyone, being able to focus solely on the frontmost window can be a nice productivity helper. All the other windows, no matter how much they are crying for you to visit them, just seem a little less important when they're faded out. You can choose how transparent background windows become with HazeOver, and even enable it and disable it with a quick checkbox. We'd love it if it had a few more features—like the ability to ignore certain programs—but overall, it works rather well, and the fading animation is some nice eye candy to boot.
If you'd rather not have an app fade your windows automatically, previously mentioned Afloat will let you manually fade windows in and out that you don't need to see. And, of course, if you're a Windows user, you can do this with a simple AutoHotkey script.
HazeOver is a $US0.99 download for Mac OS X.