* You pick one up in the Burned Tower when you have defeated all of the Executives that are at the Team Rocket HQ.
* You can also get a Master Ball inside a Poké Ball as a daily gift from the girl inside the house to the left of the Indigo Plateau Pokémon League.
* Once you have unlocked Saffron City, there's a guy in the Pokémon Fan Club who will trade a Master Ball for a Gengar.