Salamence debuted in Mutiny in the Bounty!, the same episode as its Trainer. It mostly serves as J's mode of transportation while she is not in her airship. It is also frequently used in battle.
In Ill-Will Hunting!, J used Salamence and her Drapion to battle Ash's Pikachu and Gary's Blastoise.
J tends to use Salamence for destructive purposes as well. In Pokémon Ranger and the Kidnapped Riolu! (Part 1), she commanded it to destroy a forest with its Flamethrower to smoke out the Riolu she wanted to capture.
Later, in Pillars of Friendship!, J used its Hyper Beam to knock down the rock, ice, and steel pillars inside the Snowpoint Temple and Flamethrower to awaken Regigigas. Salamence is also able to hold its own in battle against legendary Pokémon such as Regigigas and also could evade a volley of Hyper Beams from Brandon's Regirock, Registeel, and Regice with ease.
In The Needs of the Three!, it was used by J to get Uxie, Mesprit, and Azelf for Team Galactic. What happened to Salamence after the destruction of J's ship is unknown.
In Memories are Made of Bliss!, Team Rocket's fantasy featured Salamence with J riding it.