* One of the ponies [[spoiler: Nightmare Moon]] tried to recruit for her QuirkyMinibossSquad during her [[spoiler: initial rampage]] was [[spoiler: [[VideoGame/StoryOfTheBlanks Ruby]].]]
* One of Trixie's memories is of speaking with a counselor with a resemblance to "Franchise/HarryPotter".
* A lot of MLP Fanfictions are referred to, existing either as alternate realities, in-fic canon, in-fic ghost stories, or [[BreakingTheFourthWall Pinkie Pie telling us to stop talking about]] [[Fanfic/{{Cupcakes}} that stupid fanfic.]]
** In the same story, Pinkie mentions an anime called [[Manga/{{Naruto}} "Narutrot"]]
** ''Cupcakes'' is referenced again in the illustrations for the BadFuture's audio adaptation. This time, it's [[spoiler: ''Fluttercruel'']] who's pulling it off.
** After Rainbow Dash snaps at Scootaloo in a short fit of anger, the filly gets afraid that [[FanFic/RainbowFactory 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. CrowningMomentOfHeartwarming and TakeThat masterfully combined.
* In the "Penultimate Beta 1" Chapter (AKA [[spoiler:Fluttercruel POV Black Pearl]]), one of the tabloid articles Luna mentions claims that Luna was turned into Nightmare Moon because she was [[Literature/{{Animorphs}} infested by an evil mind control slug]].
** Could also be talking about [[Series/StargateSG1 Goa'uld]] or be a reference to [[{{Futurama}} Brain Slugs.]]
** [[spoiler: Fluttercruel]] tells Fluttershy that she would love it [[FanFic/{{Pattycakes}} if she could take Rainbow Dash's mind and reduce it to that of a newborn filly.]]
*** Also, [[spoiler:Fluttercruel]]'s speeches to Fluttershy are based off of [[spoiler:[[Manga/{{Bleach}} Ichigo and his Hollow]]'s]].
** Darwin The Dragon's law is mentioned which is obviously a reference to CharlesDarwin.
* During Luna's confrontations with Discord, he says that he had to tell the same lesson to "A bald man," long ago. Doubles as a shout-out to the voice actor, but also subtly implies that [[Series/StarTrekTheNextGeneration Discord IS Q.]]
* Doctor Whooves' discorded version basically becomes [[Recap/DoctorWhoS30E17E18TheEndOfTime Rassillon.]]
* One of [[spoiler:Princess Gaia]]'s brainwashing melodies is "Come Little Children" from ''HocusPocus''.
** Also, [[spoiler:Princess Gaia]]'s plan to [[UtopiaJustifiesTheMeans save everypony by turning them all into foals]] harks back to a [[NightmareFuel very nasty]] [[FanFic/{{Pattycakes}} fanfic]] in which [[spoiler:Fluttershy]] did ''precisely that'' to her fellow ponies.
* Upon seeing the Midsummer's Night Sisters' SuperSentaiStance, Twilight mentions it reminded her of something out of ''[[Series/MightyMorphinPowerRangers Mighty Morphing Pony Rangers]]''. Their name is of course a refrence to ''AMidSummerNightsDream''.
* In "Links", Twilight and [[spoiler:Trixie]] are reading ''[[Literature/HarryPotterAndTheDeathlyHallows Harry Trotter and the Lunar Hollows]]''. Twilight wonders if the writer actually talked to any real magic users for the book.
* The Side-Story, where Luna is in a play, the story she tells is very clearly [[Literature/HarryPotterAndTheDeathlyHallows The Tale of]] [[TheTalesOfBeedleTheBard the 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.
** [[spoiler: Turns out, like the Tale of the Three Brothers, this is real. The horn is actually called "The Elder Horn."]]
* One young pegasus in "Everkind Forest" is [[Franchise/TheLegendOfZelda Link]], who, in this timeline, has been granted a peaceful, happy life as a pony as a reward for [[EarnYourHappyEnding all the battles he's had to fight throughout history]]. "Pearl Necklace Part 3" introduces his girlfriend, a green pegasus named [[VideoGame/TheLegendOfZeldaOcarinaOfTime Saria]].
* The song [[spoiler: brainwashed]] Cherilee sings [[spoiler:while battling the heroes]], ''Teacher Teacher'', is obviously modeled on [[NoMoreHeroes Margaret Moonlight's]] ''Philistine''.
** Celestia's song [[spoiler:that she uses to unbrainwash Princess Gaia/Nightmare Whisper's foals]] is the G1 ''MyLittlePony'' theme song.
* The title of the chapter "The Foal of Omelas" references the story "Those Who Walk Away From Omelas". [[spoiler: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 [[spoiler:Trixie and Fluttercruel being Elements of Harmony.]]
--> '''Rainbow Dash''': Is this gonna be like buckin' [[DragonBallZ DragonEggs Z]] where everybody [[spoiler: get an Element]]?!
--> '''Pinkie Pie''': Nah, pretty sure this is like [[Series/PowerRangersRPM Pony Rangers RPM]], when the [[spoiler:[[SixthRanger two other Rangers shows up]] and make the team stronger]], silly!
* [[spoiler:One of Luna's middle names is [[FanFic/PastSins Nyx]].]]
** [[spoiler: Alternatively, Nyx is the [[ClassicalMythology Ancient Greek Titan of the Night]]. Additionally, one of Princess Celestia's middle names is Amaterasu, [[JapaneseMythology the Shinto goddess of the sun]].]]
** [[spoiler: In a more definite shout out to ''FanFic/PastSins'', 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.]]
* [[spoiler:Discord's brother Anarchy is causing chaos to combat entropy. [[Anime/PuellaMagiMadokaMagica Sound familiar]]?]]
** Also, this might count as an ActorAllusion, [[spoiler: the author gives Anarchy's voice actor as Creator/QuintonFlynn, and makes a lot of nods to KingdomHearts.]]
* Fluttershy's [[spoiler: transformation into Princess Gaia]] mirror's [[Anime/PuellaMagiMadokaMagica Sayaka's]] [[spoiler: transformation into a Witch.]] It helps that both scenes have the horrified bystander [[SayMyName screaming out their friend's name]] as it happens.
** On a similar note, [[spoiler:Nightmare Whisper]]'s [[LotusEaterMachine goals]] closely resemble those of [[spoiler:Kriemhild Gretchen, Madoka's Witch form, as described in [[AllThereInTheManual supplementary material]].]]
** Also, two of the Virgacorns who died in the Apple Pie chapter of the Dark World arc were named Puella and Magica.
* Inverted with ''FanFic/GettingBackOnYourHooves'', which has [[spoiler:Discord's manner of [[BreakTheCutie breaking Trixie]] during his reign]] be the same as it is in this series as a homage to it.
** The Blog/AskAPony Blog ''[[http://askponydiscord.tumblr.com/ Ask Pony Discord]]'' by the same author has referenced the fic a number of times. At one point, while Discord is discussing [[TheEarthPrimeTheory what happens if Canon!Discord shows up in the Heart World]], Heart World is even followed by (© of Alexwarlorn).
* In her second side-story, Luna states that there was an "[[NoodleIncident incident involving some kitchen appliances]]" [[{{Progress}} drove her catch up on the times]].
* Celestia's [[spoiler:speech to Luna before revealing [[OneWingedAngel her Orion form]]]] is a ShoutOut to the ''Series/StarTrekDeepSpaceNine'' episode "The Way Of The Warrior" when [[spoiler: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 Universe}}s she sees upon [[spoiler:looking into herself/the Gate of Truth again]] are fanfic references.
** One of the Alternate Universes shows a WhatIf scenario where [[spoiler:Pinkie Pie becomes Nightmare Granfalloon]]. This is immediately followed up with a scene akin to one in Episode 10 of ''Anime/PuellaMagiMadokaMagica'', wherein [[spoiler:Mami[=/=]Rarity freaks out at the AwfulTruth]].
** One of the Alternate Universes has a pony version of the FinalBattle of season 1 of ''Series/MightyMorphinPowerRangers'', with the mane cast as the rangers and Gilda as Goldar. Incidently, ''Mighty Morphing Power Ponies'' is frequently mentioned as a [[ShowWithinAShow Show Within A Fanfic]] throughout the fic.
** Another alternate reality seen has the mane cast becoming KnightTemplar dictators of their world using the Elements of harmony where any sign of disharmony or unhappyness is treated with brainwashing and other brutal methiods, a ShoutOut to the [[JusticeLeague Justice Lords]]. In fact, WordOfGod has said they [[WhatCouldHaveBeen originally wanted to call them the Harmony Lords]] but changed it to Harmony Queens due to gender.
** A recent edit revealed what AJ ended up becoming the Element of Laughter: [[spoiler: [[MyLittlePonyTVSpecials 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 [[CodeGeass "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, [[spoiler:Fluttershy's stare turns out to be one]].
* Rarity's thoughts during her discording are reminiscent of a [[VideoGame/BioShock1 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!'
* In "Cruel's Best Pet":
--> "A beehive!", Shy thought suddenly.
--> "[[TheWickerMan NO, NOT THE BEES!]]"
* In "Generational Transitions"
--> [[spoiler:'''Strife''']]: [[IndianaJonesAndTheLastCrusade You have choosen...wisely.]]
* When Diamond Tiara [[spoiler:becomes completely corrupted by Discord and [[SuperpoweredEvilSide goes Nightmare]], her Cutie Mark becomes [[TabletopGame/{{Warhammer 40000}} the Star of Chaos]]]].
** It's also strongly implied in the new [[BadFuture Epilogue]] chapters that Discord's Equestria was attacked by [[AlienInvasion alien invaders]]. After defeating them, Discord went to their ruler to toss a cream pie into his face... only to discover their ruler was [[TabletopGame/{{Warhammer 40000}} a sick old man on life support]].
* When Discord is explaining to [[spoiler: Diamond Tiara]] that insanity [[InTheBlood runs in her family]] and lists a few of her notable ancestors -- one apparently wrote the pony version of TheKingInYellow, and another wrote the pony version of the [[CthulhuMythos Necronomicon]]. Speaking of which, Discord also offhandedly mentions his "cousin Ponythulhu".
* In "DarkestHour", Cadence tells Twilight Tragedy that "[[GaoGaiGar destruction is the hope for a fresh start from zero]]".
** During that same fight, when Cadence asks Rarigreed why she's serving Discord, she responds with a modified version of the fanon [[Franchise/GreenLantern Orange Lantern oath]].
* When Shining is describing his dreams in "ecnarbmemeR-Remembrance", one of them is a shout out to ''Film/TheAvengers'' (with Shining himself in the role of NickFury), with another being a shout out to ''VideoGame/FinalFantasyIV''. Later on in the chapter, when Twilight is telling him about Nightmare Moon's impending return, he responds with two BigWhat-s followed by a FlatWhat, a'la [[Series/DoctorWho the Doctor]].
* "Modern Major EvilOverlord" is pretty much a {{Deconstruction}} and {{Parody}} of the ''EvilOverlordList''. Not to mention a shout to Creator/GilbertAndSullivan's famous [[Theatre/ThePiratesOfPenzance "Modern Major General"]]. Who knew Discord was a fan of light opera?
* [[spoiler:The circle of ponies circling Twilight near the end of Party At Canterlot Castle/Daybreak]] could refer to either the TV ending of Anime/NeonGenesisEvangelion and a scene in the RecapEpisode of ''[[Manga/FullmetalAlchemist Fullmetal Alchemist: Brotherhood.]]''
* In "Apple Tree" one of the worlds is Twilight and Discord reenacting the [[spoiler:filming of the]] FinalBattle between [[GaoGaiGar GaoGaiGar and Palperapa]], with Twilight as Guy and Discord as Palperapa. We also see that Rainbow Dash is [[spoiler:playing]] J.
* In Part 8 of Dark World, Fluttercruel and Discord are at one point seen playing ''VideoGame/SpaceInvaders''.
* Discord in Part 8 of Dark World also mentions that there's an AbandonedWarehouseDistrict specifically so he can have giant monster fights without '[[PragmaticVillainy breaking his toys]]' in the process, even telling Fluttercruel she needs to watch more [[Franchise/PowerRangers Pony Rangers]] since she didn't understand.
* When Twilight confronts Rarigreed in her mind, she makes statements very similar to when Ling calls out Greed in ''Manga/FullmetalAlchemist''.
--> '''Twilight''': A mare willing to throw away something precious to her has no right to call herself Greed!
* Dark World Part 11 briefly shows Anarchy feeding a pony version of [[Film/TheDarkKnightSaga Bane]] his lines during his big speech.
** Chapter 22 has a flashback to Discord giving a similar speech when taking over Manehatten and driving everypony crazy. It also has a similar KangarooCourt to the movie's.
* Santa Hooves [[BadassSanta breaking into Discord's castle yearly]] in the [[BadFuture Dark World]] timeline has been confirmed by WordOfGod to have been based off [[http://tytempletonart.wordpress.com/2009/12/22/a-little-pre-christmas-gift-from-ty/ this comic]] where Santa Claus does it to Darkseid (the occurrence) and the British ''SonicTheHedgehog'' comics were Robotnik gets the visit (his NighInvulnerable qualities and justification for them).
* When the new Mane Six go after Discord in Dark World 14, one of the Apple/Pie clan cheer them off with "[[Film/ThePrincessBride Have fun defeating the evil overlord!]]"
* Derpy's "go sideways!" comment in "Six Points Of Light" was one to [[http://www.youtube.com/watch?v=tJBihKiuWv0 this video.]]
* During a flashback in part 3 of Shining Armor's arc, Twilight reads a tabloid story about fears that [[Franchise/HarryPotter Hogwarts]] and [[Literature/{{Discworld}} the Unseen University]] will soon surpass Celestia's school.
* The head of Cadence's contingent of Air Naval Cavalry is [[Franchise/{{Halo}} Master Chief Petty Officer Spartan]], while the captain of the ship she & Shining Armor are traveling on is a mare named [[Franchise/MassEffect Shepard]], whose XO is a Commander [[Franchise/JamesBond Bond]] (who is later revealed to be in Intelligence).
* Part 4 of Shining Armor's arc is chock full of references: the Griffins have an [[AirborneAircraftCarrier Airborne Airship Carrier]] called the ''[[Franchise/BattlestarGalactica Galactica]]'' and a couple of [[Franchise/MassEffect Reaper]]-class ships called "Sovereign" and "Harbinger". Shining mentions a "Community Service Initiative" agent in Miamhay who keeps "[[Series/CSIMiami making bad puns and putting on sunglasses]]". Among the Hooviets, Shining Armor meets two named [[VideoGame/CallOfDutyBlackOps Mason and Reznov]], while the Hooviet leader has the surname [[ModernWarfare Makarov]]. And later, when General-Admiral Makarov makes his big entrance, someone (presumably one of the nearby Hooviet expatriates), comments that everyone keeps forgetting that "[[Film/CaptainAmericaTheFirstAvenger the first tribe the Hooviets conquered was their own]]". And oh yes, they have a military officer with them named {{Sharpe}} who [[LampshadeHanging speaks with a British accent.]]
* 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 "[[Series/DoctorWho I am the Master, and you will obey!]]"
** [[WordOfGod The author of that chapter]] has also stated that Patch and Buddy's relationship is based on Amy and Rory's, as another shout out.
* Shining Armor part 5 reveals that some of the other ships in Cadence's floatilla are commanded by ponies named [[Series/StarTrekDeepSpaceNine Sisko]], [[Series/StarTrekEnterprise Archer]], and [[Franchise/StarWars Solo]].
** There's also a couple of pilots named [[Series/{{Firefly}} Washburn and River]].
** In part 6, he references a game called "[[VideoGame/CallOfDuty Call of Cutie]]", and is later aided by the griffin special forces [[Franchise/MetalGear Metal unit]].
** There's also Makarov's [[VideoGame/MetalGearSolid3SnakeEater Shagohods]], which are actually more like [[Literature/TheWarOfTheWorlds Martian Tripods]]. For bonus points, they're fought by Thunderchild, though he survives, unlike the ship.
* In Dark World 18, there's a heavy thematic reference to ''ComicBook/WhateverHappenedToTheManOfTomorrow'' and what it means in relation to TheQuest they are on.
** Also, the chapter is called "[[Recap/DoctorWhoS23E4TheUltimateFoe The Ultimate Foe]]", the name of the last serial of the "Trial of a Time Lord" story arc of the [[Series/DoctorWho classic series]] that the Valeyard first showed up in.
* Shining Armor 7: The Griffin General is named [[VideoGame/ModernWarfare Goldeagle Shepherd]].
** Minutte also makes direct reference to ''Film/TheSixthSense''. Bonus points for also being a TakeThat.
* According to Discord in Dark World 19, one of Havoc's titles is [[Manga/{{Dragonball}} Home For Infinite Losers]].
* One exclusive to the AudioAdaptation, the super fast Pegasi that take Twilight to Hoofington in Episode 6 are dressed like [[TheFlash the original Flash]].
* Dark World includes a direct shout-out to the 9th Doctor as Twilight confronts Angry Pie.
* In [[http://alexwarlorn.deviantart.com/#/d5nx1bf Shining Armor Chapter 8 Pt. 2]] we get a number of amusing shout outs, including one to [[Literature/TheWarOfTheWorlds Thunderchild taking out the Hooviet Tripods]] which doubles as an IncrediblyLamePun if you remember [[DirtyCommies what the Hooviets Real World inspiration were called]]; and comments on several warring factions in a nation that used to hire Diamond Dog mercenaries. factions with names like [[{{WCW}} the New World Order]] and [[Wrestling/{{WWE}} Nation of Domination and the Radicals]].
* In ''Off Da Rails'', Rancor tells the group to watch her "go [[DragonBallZ Dragon Eggs Z]]" right before she [[spoiler:transforms into her adult form]]. This may have even been a more direct reference to Cell, since [[spoiler:Rancor could only mature into an adult by absorbing Destruction's essence.]]
* In Shining Armor part 9, Shining and Cadence meet with Cadence's friend, [[CodeGeass Princess Euphie of Neighpon]], whose security detail includes a group of ninja named [[Anime/DigimonAdventure Taichi, Hikari, Takeru,]] and [[Anime/DigimonAdventure02 Daisuke]].
* The trial in Starlight's Nightmares Chapter has several shoutouts to the ''Franchise/AceAttorney'' series, including the classic 'OBJECTION!', in this case shouted by Starlight's defense attorney.
* [[spoiler:Dark World!Discord's death]] is almost identical to [[spoiler:[[BigBad Father's]] in ''Manga/FullmetalAlchemist'' WordOfGod has even confirmed it was inspired by it.
* When [[spoiler: Twilight's Nightmare]] reveals herself, she sings a variant on [[Disney/{{Tangled}} "What Once Was Mine"]].
* [[spoiler: [[TheVoice The Nameless Passenger's]]]] origins is a reference to the ending of the [[StartofDarkness Medieval Chapter]] of VideoGame/LiveALive.
** [[spoiler:She]] may also be a reference to [[spoiler:Kriemhild Gretchen]] from ''Anime/PuellaMagiMadokaMagica'' being [[spoiler:the SuperpoweredEvilSide 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 DarkMessiah believing she's working towards a better world, which is also true of Kriemhild Gretchen.]]
*** [[spoiler: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.]]
* In Shining Armor Part 11, Shining, while mentioning another crazy rule involving Princesses, mentions they would soon be joined by [[Fanfic/{{Progress}} 'princesses must learn the proper use of modern household appliances']] thanks to Princess Luna.
** Shining also mentions a Diamond Dog chief engineer named [[Series/StarTrekTheOriginalSeries Scottie]].
* In Duel of Tears, [[spoiler:after Twilight's {{Emergency Transformation}} into Half-Light Noon]] the following reference to {{G Gundam}} is made:
--> '''Rancor''': Now [[spoiler: Pegasus]] fight!
-->'''Twilight''': Ready!
--> [[spoiler: '''Nightmare Paradox''']]:(Go!)
** Likewise, Rancor says the following line in The Ultimate Foe:
--> And you've given me a passionate fight by both sides my little ponies, -whoa that's fun to say- your love, your anger, and all of your sorrow laid bare!
* [[spoiler: In one {{Groundhog Day Loop}}]], Twilight, instead of killing Discord, [[Series/PowerRangersSPD cuts off his one remaining fang. After she had done that, she said, "Now they match..."]]
** [[spoiler: In another {{Groundhog Day Loop}}, she takes the previously mentioned {{Shout Out}} {{Up to Eleven}} by doing the same thing to his horn, since Apple Pie had already managed to make him lose one of his horns in her {{Dying Moment of Awesome}}.]]
** At one point [[spoiler:Discord tells the Nameless Passenger/Nightmare Eclipse he hates her. [[DragonBallZ She replies with a variant of Trunks' speech to the Androids after he returned to the future on a]] RoaringRampageOfRevenge.]]
* When we learn about how [[spoiler: Golden Tiara/Screw Ball's]] went insane in the "Butterflies" series there is a reference to {{The Yellow Wallpaper}} which is also about a woman descending into madness.
--> I began to have strange dreams too, like that one time I thought I saw a mare moving behind the pattern on our wallpaper… I had it torn down and replaced. It was an ugly yellow anyway.
* Shining Armor part 12 shows the usual restraint for references...
** Three British Comedies are referenced by Private Ranger's horrifying advice-seeking session: [[Series/BlackAdder Squadron Commander The Lord Flashheart]] emerges as [[Series/TheMightyBoosh an erotic adventurer of the most deranged kind]] and advises ''[[NoodleImplements something]]'' with [[Series/AlloAllo a flying helmet, wet celery, and an egg whisk]]. Private Baldrick is also noted as having worked for Lord Blackadder for another reference.
** The "Bread Cannons" are a reference to a real German field kitchen from the 1890s's dubbed a Goulash Cannon for the way it resembled a cannon when the stovepipes were folded for transport.
** The bottle-lights used by the Zebra are a real invention used in the Philippines. The [[Videogame/MetalGearSolid3SnakeEater glowing mushrooms]] sometimes used as an alternative do not recharge batteries though - [[RealityEnsues they just cause stomach problems]]. MGS gets another mention with[[Videogame/MetalGearSolidPeaceWalker references to a tank-shaped cardboard box]] complete with an ActorAllusion of [[TaraStrong Twilight Sparkle]] voicing approval of the idea, just like Paz.
** Shining reckons [[Gremlins2TheNewBatch canned food and shotguns]] are a good thing to invest in for the apocalypse.
** In the arcade scene, the [[VideoGame/TeamFortress2 Dubyaplus M1 flamethrower]] is seen as somewhat noobish by Shining, and Audience earns a [[VideoGame/UnrealTournament Holy Horseapples]] from all the kills he racks up.
** The elite 18th Pegasus Legion, and the 82nd Regiment that is a part of it, are intended as references to the [[YanksWithTanks American XVIII Airborne Corps]] and the famous [[ItsRainingMen 82nd All-American Division of paratroopers]].
* Part 13 is at it too.
** The Prime Minister of Zebrawa is [[ComicBook/BlackPanther named T'Challa, is from a village called Wakanda, and has pet panthers]].
** The professor who's finds were destroyed is named ProfessorElemental. Also, the archaeology student who informs him his assistant has woken up is named [[Series/KamenRiderWizard Nitoh and has a Cutie Mark of a Chimera.]]
** 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 [[Main/{{Taggart}} Triggert]] in Clydesdale. Complete with a near impenetrable FunetikAksent that even Shining has to be on his guard with despite experience in understanding [[ViolentGlaswegian Baseplate]].
** Side Chapter 13.5 also has some moments. "[[Main/SavingPrivateRyan Five Pegasi is a juicy opportunity, one Pegasus is a waste of ammo]]", Light airships called [[Main/CommandAndConquer Orcas]] were apparently moments away from being involved against Spike in [[Recap/MyLittlePonyFriendshipIsMagicS2E10SecretOfMyExcess Secret of My Excess]], "[[Series/RedDwarf No member of the Guard should ever report for active duty in a ginger toupee]]", and as well as Quidditch, Calvinball is popular amongst the Guardsponies.
* Rainbow Dash's flying lesson to Scootaloo was a shout out to [[http://www.fimfiction.net/story/960/maiden-flight this fic.]]
* The ArcWords for the Shining Armor arc are [[VideoGame/PrinceOfPersiaTheSandsOfTime Time is an ocean in a storm.]]
* In the Dark World, [[spoiler: the Elements of Chaos basically were [[{{Naruto}} The Six Paths of Discord.]]]]
* 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. [[WordOfGod According to Godzillawolf]] this was inspired by ''WesternAnimation/ThePowerpuffGirls'' episode 'Boogie Frights', specifically the Professor telling Bubbles being brave is doing what you're afraid of.
** After [[spoiler:breaking Pinkie out of her HeroicBSOD upon finding out she was an ImaginaryFriend given life by the world changing spell]], Luna mentioned [[Creator/LaurenFaust Her Mother]] once helped Pandora create a [[WesternAnimation/FostersHomeForImaginaryFriends distant world were everyone's imaginary friends became real.]]
* Celestia states that spending the Gaia Festival with Twilight in disguise is much more fun than the time she [[Fanfic/PrincessCelestiaGetsMugged let herself get kidnapped]].
* [[spoiler: Nightmare Paradox]]'s judgement by Rota Fortuna is apparently based on [[Manga/FullmetalAlchemist Father's judgement by the Truth]].
** According to Godzillawolf, he edited the [[spoiler:attack on the Nightmares that's actually a feint to set up their final blow]] to be a shout out to the ending of ''Anime/GaoGaiGar FINAL'', which he's a fan of.
* According to RecursiveFanfiction, Film/{{Pumpkinhead}} is one of Rancor's Champions.
** That same chapter has Discord mention Strife's latest pet project of seeing how [[Film/PacificRim ponies using giant robots to fight monsters from another dimension]] would turn out.
* Chapter 14 of Shining Armor has a bunch of stuff [[spoiler: from another world]] that's examined by Misfit [[spoiler: and [[DoctorWho The Doctor.]]]] One of those items is a computer that suddenly starts playing [[Series/KamenRiderDenO Double Action Gaoh Form.]]
* And in chapter 15, when they meet [[spoiler: [[BigGood Mother Deer]] and the deer who serve her as LaResistance against the [[TheEmpire Hooviets]], one of the members is named Dima, and his WeaponOfChoice is the [[Series/TensouSentaiGoseiger Leon Laser.]]]]
* In chapter 15, when Shining Armor is in the sickbay, the name of the doctor treating him is [[Series/ZyudenSentaiKyoryuger Ulshade.]]
* [[Literature/PeterPan Pony Pan]] is mentioned several times during Sapphire Shores during her bonus chapter. Discord also finishes his BreakingLecture by asking her to " [[Music/{{Metallica}} take my hand, and come off to Never Never Land.]]"
* Shining Armor 16 includes
** Civilian ships with flags of convenience including the ''Svoboda'' flagged in [[SelfDemonstrating/DoctorDoom Latveria]] and the ''[[Main/LordOfWar Kono]]'' flagged in the Neighverlands.
** Maasailand, an ominous secretive state where an AncientConspiracy [[Videogame/CommandAndConquer called The Brotherhood are in power]]. Everything is red and black, covered in scorpion symbols, and they await their messiah. They also have spooky GasMaskMooks backing up Inquisitor-Cardinal [[Main/ThatMitchellAndWebbLook Vectron]]. [[spoiler: The entire nation turns out to be pacifists, and everyone else is simply unable to realise DarkIsNotEvil. They do not help matters with all the red glowing stuff, the easy to misinterpret language, or [[DeathbringerTheAdorable The Manticore of Peace and Happiness called Aaargh]].]] [[note]]The Manticore was in the Back Seat the whole time.[[/note]]
** The (former Kingdom) [[PeoplesRepublicOfTyranny People's]] Greater Good Of [[Discworld/{{Pyramids}} Djelibeybi]].
** Hedgehog racing [[Franchise/SonicTheHedgehog with blue hedgehogs.]]
** The Hooviets were found performing a poorly-written propaganda piece in the style of the [[WesternAnimation/AvatarTheLastAirbender Ember Island players.]] Celestia's troll tendencies were turned UpToEleven (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.
* The final part of Shining Armor 17 is titled "Come Undone", the same as the final episode of ''WesternAnimation/ScoobyDooMysteryIncorporated''. [[spoiler:Fittingly, both involve the BigBad EldritchAbomination being [[RetGone erased from existence]] along with their influence and taint.]]
* In 18.1, Commander Bond'sh father, who ish alive in the repaired timeline, continuesh his son'sh Jamesh Bond shoutouts by being an expy of Creator/SeanConnery, right down to the shpeech quirk.
* [[TheDayToday Wabznasm and Manford Thirty-Sixborough]] are mentioned by Garnet and Gag, respectively, in 18.2
* In 20 Gag talks about a Manega called [[Anime/PuellaMagiMadokaMagica Penumbra Magical Filly Madoka]]. In the next scene [[spoiler: Kyubey tries to make a contract with the CMC.]]
* Several of the alternate realities Shining sees in 21 during his fever dreams are shout outs -- among others, there's one where he's [[DragonBallZ Goku]], one that's based on ''Fanfic/OnACrossAndArrow'', and one that's a scene lifted straight from ''FanFic/RainboomsAndRoyalty''.
* In "No More Script", after mentioning a reindeer on the crew named Dasher, they mention that [[WesternAnimation/OliveTheOtherReindeer Olive, the other reindeer, is on a search and rescue team]]. Running Gag lampshades the reference by replying [[VillainSong Baw, bug and hum!]].
** There are also allusions to [[TheSecretofMonkeyIsland The Secret of Monkey Island]] and the light bulb-changing gag from ''Series/RedDwarf''.
* In "Sands of Time", Captive Audience mentions he visited Ponsia on a family holiday as a foal, and would quite like to [[VideoGame/BattlefieldThree go back to Karkand]].
* From "Explanations and Escapes" in the Wedding Arc, we have this gem of a line:
-->'''[[spoiler:Makarov]]''': [[WesternAnimation/TheSimpsons Changeling poison is]] [[spoiler:[[WesternAnimation/TheSimpsons deer]]]] [[WesternAnimation/TheSimpsons poison?!]]
* Chrysalis' endgame plan is essentially [[spoiler:[[Manga/FullmetalAlchemist Father's]]: perform a ritual using a gigantic rune that will rip something out of an entire country (in Chrysalis' case, all emotions) to become a god. WordOfGod has even stated that was the inspiration.]]
* In [[http://alexwarlorn.deviantart.com/art/Pony-POV-Wedding-Pt-10-Then-Tartarus-Broke-Loose-441701157 Chapter 10 of the Wedding Arc]], Pinkie looks into Chrysalis' soul and sees an image of [[TheSimpsons Chrysalis in a devil suit dancing around her own grave, with the headstone bearing wings and a halo]].
* The audio version of Trixie's [[spoiler:reharmonization]], we see the image of a [[FantasticRacism fantastic racist]] who resembles [[Franchise/HarryPotter a ponified Lucius Malfoy]].
* "Cadence vs. Cadenza" makes the ShoutOut that everyone had been hoping for at the end:
-->'''Shining''': [[Anime/GGundam These hearts of ours burn red! Their loud roar tells us-]]
-->'''Cadence''': To grasp happiness!
* The Mane Six's confrontation with [[spoiler:General Lone Ranger]] is one long one to SupermanVsTheElite, right down to some of Manchester Black's lines being quoted. Rarity even mentions her [[spoiler:pretending to buy into Lone Ranger's mentality]] was possibly inspired by the pony version of the comic.