I've seen a few people create custom racks and things of that nature. I don't have the ability to upload photos (I'm at work) but I know there was a few pics going around in a thread somewhere.
One simple method is to just buy a big piece of pegboard from home depot or somewhere. You can buy plastic or rubber coated hooks (so the controllers don't get scratched) and hang them on those. The U-shaped hooks I'm referring to work great for any Dualshock controllers or Xbox Controllers but might have a little difficulty with NES controllers because of the shape. You can also get hooks like that, that drill directly into a wall or piece of wood.
Only other thing that pops in my mind quickly is a hat rack, one of those long ones that run vertically and are designed to hang several hats straight up and down, if the hooks are sturdy enough you might be able to hang controllers from them or use a rubber band to loop the coiled wiring to the hook.
I know you wanted boxed and out of sight, but to me that's the equivalent of sticking them in a drawer somewhere and the only thing I can think of as far as organizing that way would be to have some kind of silverware partitions or something that allow you to separate things into individual spaces.
