In the first chapter alone, Twilight Sparkle tries and fails to point out the many, many problems with a rumor that Scootaloo is the daughter of Applejack and Rarity as it's told to her in the form of a melodramatically overwrought ship-fic.
In the second, Spike tells her about how Scootaloo's "actually" a trained-from-foalhood super spy, similarly assaulting Twilight's sanity.
Iron Will's story involves her being the adopted daughter of Gilda and Trixie (who met each other at a support group for antagonists who had been run out of Ponyville by the Elements of Harmony, along with Flim, Flam, the red dragon, and the statue of Discord, somehow). It quickly turns into an thinly-veiled plug for Iron Will's new book.
The Running Gag that everypony thinks Twilight is (somehow) the daughter of Nightmare Moon. By the fourth chapter, even she seems to be starting to wonder a little.
As of the seventh chapter, Celestia, Cadence and Luna herself now believe it.
From Chapter 5 Chicken-Loo, what's the matter with you? You don't act like other chickens do. You wear a disguise To fool pony eyes But your not a mare You're a Chicken-Loo!
The other Running Gag that everyone brings up the weird thing Twilight does when she eats a brownie.
Chapter 10 is essentially a retelling of the pilot episode of the original Power Rangers, but with Nightmare Moon as Rita Repulsa, and it turns out CELESTIA is Nightmare Moon.
Also, Pinkie Pie apparently once ran into the Equestrian equivalent of the KU KLUX KLAN. I swear to God, I am NOT making this up.
In Chapter 11, Twilight escapes from Canterlot by declaring that she's about to break a promise to a friend. As if on cue, Pinkie bursts out of a potted plant to yell "FOREVER!" but Twilight cuts her off and uses Pinkie's teleportation to get home - though not without a strange detour through the "Take on Me" video.
Shining Armor's rendition of Akon's I Just Had Sex. First it's just Shining Armor. Then Cadence joins him, making it "WE JUST HAD SEX!", THEN they sing that anyone who had sex in the past thirty minutes is qualified to sing along. Cue Cadence, Shining, Derpy, the Doctor, Tydal, half of the Wonderbolts, Gilda and Trixie all singing:
WE JUST HAD SEX!
And it felt so good!
A mare let a stallion put his junk inside of her!
We just had sex!
And we'll never go back!
To not having sex is a thing of the past!
In Chapter 13, defender2222 appears in Twilight's kitchen and tells a story that involves Lauren Faust deciding to never give Scootaloo any backstory deliberately to troll the fans, much to Meghan McCarthy's shock. This is followed by an Evil Laugh and a random appearance by a mini-Lauren.
defender2222: And that is how Equestria was made. God, I've waited a long time to say that!
In Chapter 15, Twilight runs into a broom closet on a Dalek battlecruiser to escape from yet another Scootaloo story - where she finds a sobbing Dalek.
Twisty Tail: Wait, Twilight's in the closet? So she's a thespian? Does that mean Twilight's dating her universe's version of Rainbow Blitz?
The Professor: I don't think thespian is the word you are looking for.
Twlight: I am not dating Rainbow Dash and I am not in the closet!
Dalek: Dalek not either!
Twilight: Right, no Daleks or ponies in here! Just brooms!
Dalek: We are brooms!
By the end of the chapter, Twilight has named said Dalek "Rollypolly" and brought it home, where it proceeds to "Glompinate" a terrified Spike.
As well as the Professor's reaction to this:
The Professor: Sweet Lordess, they're bonding...
Also, the Professor's story, in which both Pinkie Pie and Berry Bubble warp onto the TARDIS after Twisty makes a comment about hurt feelings and losing friends. The Professor confines both Pinkie and Berry to a closet while she figures out how to send them home. This does not go how she planned. At this point Applejack joins Twilight and Rollypolly in their closet. Then, Pinkie is found to be pregnant, and Booster Gold and Blue Beetle arrive to prevent the Professor from doing something to stop Scootaloo and her gender-swapped twin Rollalong from being born.
When Spike tries to debunk their claim that he's a vampire by pointing out that he's out in the sun, Bon Bon walks by and claims that "Vampires sparkle in the sunlight!" Cue a "NO THEY DON'T!" - several font sizes bigger than normal - from every stallion and colt in a three block radius.
Even better given Twilight Twilight from the sequel.
The ending of Chapter 20, when Luna, Cadance, and Tydal swing by Zecora's hut with margaritas.
Twilight: You know what? I don't care. If it gets me drunk I'll be your daughter. I'll be your kid for booze. Luna: That's all I ever asked! Cadance: That is so sweet! I'm gonna make 'em kiss. Tydal: Cadence, no! Bad alicorn!
At the start of Chapter 22, Twilight dreams she is being put on trial for aggravated assault - specifically, against the various tables she's bashed her head against since the story started. And she doesn't help her case when she says "You Have to Believe Me, I don't have it in me to hurt something that can feel!" while slamming down her hoof down on the defense table in front of her - since said defense table is her lawyer. She is then punished by being transformed into a table, which Shining Armor and Cadance promptly start having sex on.
The stereotypes of Oceanic Creatures, or OCs, which correspond exactly to the fanfic term.