Loose, on the floor no less, and near your N64, also should be stored on the floor. Bonus points if you have pets who aren't potty trained and like to mark ownership on things you write your name on, you know, like Nintendo cartridges.
These things are built like tank, you can chuck them across the room full force 90 MPH and it won't do a darn thing to them. Why would you store them in some special case?