Master Ball/Manga

Movie adaptations
In , attempted to use a Master Ball to catch, but failed.

Pokémon Adventures
In And Mewtwo... Three!, Blaine was revealed to be in possession of a Master Ball. Soon afterwards, used it to catch  for Blaine.

Pokémon Diamond and Pearl Adventure!
In (Violent) Earthquake! Cyrus's Consuming Ambition, Cyrus gave Hareta a Master Ball as a recognition for him having moved his emotions, telling him to bring it with him to Mt. Coronet. In Bonds Connect Across Space-Time..., the Master Ball fell out of Hareta's pocket at the Spear Pillar, and Professor Rowan told him about its capability to catch any Pokémon without fail. In an attempt to stop the battle between and, Hareta tried to use the Master Ball to catch Palkia, but Palkia, having total control over space, was able to make itself disappear out of Master Ball's way and then smack it aside.

Pokémon Pocket Monsters
used a Master Ball in The Legendary Pokémon Appears!! to catch.

Pokémon Zensho
0 obtained a Master Ball from the Silph Co.'s president in Saffron City as a thanks for rescuing his company from the hands of Team Rocket.