This very cool mini-app for Mac OS X will help clean up your open windows without you needing to do anything! 

Spirited Away is very simple utility for MacOSX. You just start it up and let it run in the background. Spirited Away checks each running application’s activity, and if an application isn’t active for a certain fixed time, Spirited Away hides the application automatically. It is, in effect, Spirited Away 🙂

I am playing with the settings, but right now setting it to hide unused apps after three minutes seems about right for me. 

Get it here: SpiritedAway