The Master Sphere allows you to activate any attribute or ability node on the Sphere Grid. Master Spheres are kind of pretty rare, with your first ones probably being from unlocking Nemesis (you get ten from that). Outside of that, all of the Dark Aeons have a Master Sphere as their rare drop, as do Penance’s Left and Right Arm. Penance will also always drop at least three Master Spheres upon defeating it. Once you defeat the bosses mentioned above, there is no way to refight them. However, as long as you don’t defeat Dark Yojimbo the five times as needed, you could effectively farm him for Master Spheres.