Spirited Away

With Sprited Away [author, MacUpdate] you specify the maximum time of inactivity for your applications. When a program has been inactive for such a time it is automatically hidden by spirited away, so you don't have many annoying windows visible on the screen.

If there is any application you don't want to behave like this you only have to exlcude it in the top bar menu (See right image)

Spirited away doesn't have Dock icon nor interfere visually in any other place

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