How do I keep an apps muted when it's not on top?
Right now, with Windows 7, if I minimize a window it will silence that app.
There is no global setting for this.
The default behaviour of applications is not to automatically mute when minimized.
The exception to this are some games that have their sound engine/routines built in to the main game engine. The majority of full screen games completely pause their engine when minimized or they go out of focus - which is why they mute.
Again, this is not the default behaviour and any application that does this would most likely have been coded to do so. All I can suggest is to look in to the application's setting and see if you have any way to enable sound on minimization.