- The house in Onett that asks you to complete the name of a Beatles song with "Yes" or "No" has been replaced with one in North Ponyville where an unseen pony asks you who your favorite princess is... but you can still only answer "Yes" or "No"."Princess Celyestia/Princess Luno? Close enough."
- Upon getting the Element of Laughter, Applejack offers to help clear the boulders blocking the way to the next town. Upon getting there and talking to her, she'll note how there's something odd about one of the boulders... at which point you get into a boss battle with Tom. Yes, that Tom. The boulder Rarity thought was a gem when Discord brainwashed her. The kicker? It's not a Changeling!
- Many of the characters in the game have either been replaced with a background pony from the show or a more major character that only appeared in a single episode. However, certain popular NPCs from EarthBound are still in the game...as ponies. Yes, this means there are pony Mr. T lookalikes walking around areas in the game. There are also ponified New Age Retro Hippies running around too.
- Upon returning to the group with the ability to pull off the Sonic Rainboom now, Scootaloo makes mention of how Rainbow Dash said it's not quite a Sonic Rainboom yet. Like it isn't a real one yet, close, not quite, and would still take a while before she could pull a real one off. Somehow, the comment manages to be funny because it honestly does sound like something Dash would say upon finding out someone else can perform her signature move.
Funny / EquestriaBound