Let's just put it this way, anything you cannot buy from any store must be MASTERed to get more than one, except for Underwater.
Master Magic, Master Command, and Master Summon can only be gotten in two ways:
1. You fight Emerald and win to get the Earth Harp. Then, give the harp to the Kalm Traveler (2nd floor of the house at the bottom-right of Kalm).
2. You MASTER all of what you want the "Master [something]" of (i.e. to ge the Master Magic, you'll have to MASTER every green materia orb, or magic materia). The exception to this is Master Command, where you would only need to MASTER Steal, Sense, Mime, Manipulate, and some other I can't remember right now (I'm sure somebody else might fill those in).