Twilight Sparkle is a major character, so this trope is instantly in play.
Nyx is, if possible, even more adorkable. Among many other things, she becomes a huge fan of the Equestrian equivalent of The Hobbit and throws marathon screenings with her friends.
Bright Eyes, the friend Nyx makes through their shared love of Bilbo Burro (the Hobbit Expy), is this as well. They become fast friends after Nyx saves him from a Gang of Bullies who were making fun of his Bilbo Burro plushie.
Big-Lipped Alligator Moment: The series is filled with moments when the story comes to a grinding halt so that the author can spout his personal beliefs even when they have nothing to do with what is currently happening.
Hilarious in Hindsight: Pretty much any mention of Tirek (intended as a Shout-Out to the specialRescue From Midnight Castle) becomes this after the season 4 finale, where it's established that a version of Tirek really DOES exist in the Generation 4 continuity. His rampage is covered here in Tirek Gets a Righteous Beatdown.
In Nightmare Night and Nyx, Bruce Mane mentions that he's on the lookout for heroes, and it seems the Mane Six have caught his eye. Season 4 has an episode featuring the Mane Six becoming comic book superheroes briefly.
At the climax of Alicornundrum, a reformed villain of Twilight Sparkle (Nyx) works together with a jerkass unicorn from Canterlot who is no longer a jerk (Prince Blueblood), several youths from Ponyville and the young relatives of visiting foreign emissaries: among their ranks the Cutie Mark Crusaders, a Changeling, a Griffin, and a Seapony. All of them work together to help undo the insidious machinations of one pony (Duke Blueblood) against Princess Twilight Sparkle, thereby exposing that pony's treachery to the rulers of Equestria and the other nations. Now what ended up happeningin Season 8 of the show again?
low-key, but the Cosmic Synchronizer: A device meant to help control the movements of the Sun and Moon without Celestia and Lunas' direct and constant input. Season 9 shows us that Celestia and Luna had created a similar Amulet of their own design that is meant for Twilight Sparkle to use to control the Sun and Moon after the two of them retire.
In Cheerilee's Class, it's established that at some point after Twilight's coronation, she remodeled Golden Oaks Library into a full-blown tree castle. Flash forward to the Season 4 finale, where the library is destroyed and replaced with a new castle. Righteous Beatdown covers this, too, but delivers a Take That! calling the canon castle ugly and having the others finish the process to create the enormous tree castle.
The dragons who attack the Crystal Empire get beat up and go to jail, but the worst part is the aftereffects of their Fire Opals, perhaps especially for Garble.
The Diamond Dogs were pressed into service out of fear for their lives. Their punishment is relatively merciful.
Moral Event Horizon: When Garble and his gang realize they goofed, they decide to simply smash the Crystal Empire.
Narm: Nyx and the CMC make an argument against the "All Girls Like Princesses" stereotype, citing that it is sexist to assume this for every filly. While this argument would make sense in real life, in the context of the world of Equestria, which is ruled by princesses, it just comes across as nonsensical.
Nyx feels bad whenever she dwells on her unique origin. She also spends a lot of Nightmare Night in abject terror.
Flitter and her family have been starving. Flitter takes a big risk in attending the festivities for food, and her parents take a big risk in looking for her. Once their species is discovered, they beg for mercy.
Alicornundrum
Cheerilee's Class
The Woobie: Willow has a bit of this, with all the bullying he went through before he came to Ponyville.
Silver Spoon falls into Jerkass Woobie territory when the story about her is revealed.
