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.
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.
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.
Hilarious in Hindsight: At the climax of the story, 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 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. What ended up happening inSeason 8 of the show again?
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.