In the same story, Pinkie mentions an anime called "Narutrot"
Cupcakes is referenced again in the illustrations for the Bad Future's audio adaptation. This time, it's Fluttercruel who's pulling it off.
After Rainbow Dash snaps at Scootaloo in a short fit of anger, the filly gets afraid that Rainbow Dash will throw her into the "Pegasus Machine". Dash proceeds to reassure that there is no such thing as a Pegasus Machine and never will be except in stories, that if there was one Rainbow Dash herself would have been fuel for it long ago (as she was thrown out of flight school), and also that if the Factory wanted Scootaloo they'd have to go through her, Dash, in the first place. Crowning Moment of Heartwarming and Take That masterfully combined.
In the "Penultimate Beta 1" Chapter (AKA Fluttercruel POV Black Pearl), one of the tabloid articles Luna mentions claims that Luna was turned into Nightmare Moon because she was infested by an evil mind control slug.
The Side-Story, where Luna is in a play, the story she tells is very clearly The Tale ofthe Three Brothers, with a horn standing in for the Elder Wand for the eldest brother, wings for the Resurrection Stone, and a horseshoe that would give him invisibility for the third brother's Cloak of Invisibility.
Turns out, like the Tale of the Three Brothers, this is real. The horn is actually called "The Elder Horn."
The song brainwashed Cherilee sings while battling the heroes, Teacher Teacher, is obviously modeled on Margaret Moonlight'sPhilistine.
Celestia's song that she uses to unbrainwash Princess Gaia/Nightmare Whisper's foals is the G1 My Little Pony theme song.
The title of the chapter "The Foal of Omelas" references the story "Those Who Walk Away From Omelas". Nightmare Whisper actually refers to herself as "the Forsaken Foal Of Omelas" at one point, taking the suffering for all of Equestria on herself.
In "Pearl Necklace Part 4", Rainbow Dash and Pinkie Pie make these comments about Trixie and Fluttercruel being Elements of Harmony.
Rainbow Dash: Is this gonna be like buckin' DragonEggs Z where everybody get an Element?!
In a more definite shout out to Past Sins, during Origins Celestia compares Shady's raising of the young amnesiac Discord to a world she saw in the Truth where Twilight did the same for a child born of Nightmare Moon's essence.
Discord's brother Anarchy is causing chaos to combat entropy. Sound familiar?
Celestia's speech to Luna before revealing her Orion form is a Shout-Out to the Star Trek: Deep Space Nine episode "The Way Of The Warrior" when Sisko tells the Klingon fleet how they've had a year to prepare for a Dominion attack and are ready.
In "AJ's Dream", many of the Alternate Universes she sees upon looking into herself/the Gate of Truth again are fanfic references.
One of the Alternate Universes shows a What If? scenario where Pinkie Pie becomes Nightmare Granfalloon. This is immediately followed up with a scene akin to one in Episode 10 of Puella Magi Madoka Magica, wherein Mami/Rarity freaks out at the Awful Truth.
A recent edit revealed what AJ ended up becoming the Element of Laughter: G1 AJ.
Another Alternate World has Twilight Sparkle facing off with Nyx from Persona 3.
Oh, and Nyx uses the same line that she uses before she starts throwing Night Queen around.
Trixie makes a joke about Twilight "using a Geass" to make everypony fall in love with her doll at one point. Geasses are mentioned a lot in the series, actually. For example, Fluttershy's stare turns out to be one.
Rarity's thoughts during her discording are reminiscent of a certain game.
Isn't a pony entitled to the sweat of her flanks? 'No!' says Mayor Mare, 'It belongs to the poor!' 'No!' says Canterlot 'it belongs to Celestia!' 'No!' says Pinkie Pie, 'It belongs to everyone!'
It's also strongly implied in the new Epilogue chapters that Discord's Equestria was attacked by alien invaders. After defeating them, Discord went to their ruler to toss a cream pie into his face... only to discover their ruler was a sick old man on life support.
When Discord is explaining to Diamond Tiara that insanity runs in her family and lists a few of her notable ancestors — one apparently wrote the pony version of The King in Yellow, and another wrote the pony version of the Necronomicon. Speaking of which, Discord also offhandedly mentions his "cousin Ponythulhu".
During that same fight, when Cadence asks Rarigreed why she's serving Discord, she responds with a modified version of the fanon Orange Lantern oath.
When Shining is describing his dreams in "ecnarbmemeR-Remembrance", one of them is a shout out to The Avengers (with Shining himself in the role of Nick Fury), with another being a shout out to Final Fantasy IV. Later on in the chapter, when Twilight is telling him about Nightmare Moon's impending return, he responds with two Big "WHAT?!"-s followed by a Flat "What.", a'la the Doctor.
In "Apple Tree" one of the worlds is Twilight and Discord reenacting the filming of theFinal Battle between GaoGaiGar and Palperapa, with Twilight as Guy and Discord as Palperapa. We also see that Rainbow Dash is playing J.
In Part 8 of Dark World, Fluttercruel and Discord are at one point seen playing Space Invaders.
Derpy's "go sideways!" comment in "Six Points Of Light" was one to this video.
During a flashback in part 3 of Shining Armor's arc, Twilight reads a tabloid story about fears that Hogwarts and the Unseen University will soon surpass Celestia's school.
The head of Cadence's contingent of Air Naval Cavalry is Master Chief Petty Officer Spartan, while the captain of the ship she & Shining Armor are traveling on is a mare named Shepard, whose XO is a Commander Bond (who is later revealed to be in Intelligence).
In Patch's entry into "Gaiden: 7 Dreams/Nightmares", she defeats the dragon Basil and forces him to call her master. When he protests an order she gives him, she responds with "I am the Master, and you will obey!"
In Off Da Rails, Rancor tells the group to watch her "go Dragon Eggs Z" right before she transforms into her adult form. This may have even been a more direct reference to Cell, since Rancor could only mature into an adult by absorbing Destruction's essence.
She may also be a reference to Kriemhild Gretchen from Puella Magi Madoka Magica being the Superpowered Evil Side of the main character, powered up by multiple timeloops into an extremely powerful monster (only in this case, she's responsible for the loops), many of which end in her creation. In addition, she's also a Dark Messiah believing she's working towards a better world, which is also true of Kriemhild Gretchen.
She also resembles Walpurgis Night, particularly the various references to her being 'an Alicorn Witch' coming to destroy the world and being composed of multiple Nightmares merged into one, as well as being the final bady who (if Discord doesn't) causes Twilight to reset time.
Something of an Aircraft theme with some Pegasus names: The Meteor and Shooting Star were the first RAF and USAF jet fighters respectively, Supermarine refers to the manufacturer of such famous aircraft as the Spitfire.
A flashback dream recalls a meeting with Chief Inspector Triggert in Clydesdale. Complete with a near impenetrable Funetik Aksent that even Shining has to be on his guard with despite experience in understanding Baseplate.
Clover's Gaiden Story has Clover tell Shady that she's more brave because she's scared to do what she ultimately does to protect others. According to Godzillawolf this was inspired by The Powerpuff Girls episode 'Boogie Frights', specifically the Professor telling Bubbles being brave is doing what you're afraid of.
The Hooviets were found performing a poorly-written propaganda piece in the style of the Ember Island players. Celestia's troll tendencies were turned Up to Eleven (and she was also fat), Cadence was a total moron and Luna is obviously evil, while Makarov was a perfect, boring and invincible hero while Shining was the main villain and powerful enough to come back to life again just to give Makarov another chance to kill him in the play. After the play ended, Cadance got the last laugh by ordering her group to remove their disguise spells and teleporting said disguises away to make it look like they had been there the whole time, then walking right up to the stage and telling the Hooviets what an excellent parody they had created, leaving them with the choice of either correcting her, thus revealing how egotistical and jerkass they really were, or agreeing with her and letting everyone see it as the propaganda that it was, but allowing them to save face and potentially attract a bigger audience in future performances.