Applejack's name is the name of an alcoholic beverage, and the derisive nickname "Apple Teeny" that Spike gives her in Bridle Gossip is pronounced the same as "appletini," the name of another alcoholic beverage.
Derpy is named for her eyes being off-center, resembling a meme which afterward became a word.
Dr. Hooves is named after Doctor Who, and though his resemblance to the 10th Doctor (portrayed by David Tennant) was at first only coincidental, he has been depicted similarly in various official material. In some material he wears a green or red necktie and/or the 10th Doctor's outfit.
Las Pegasus is a play on the city of Las Vegas, though the writer of the episode felt that the latter was not a very successful pun, and it was eventually re-interpreted in the map of Equestria poster as Los Pegasus, then later changed to Las Pegasus on a newer map.
The show features dragons, griffons, unicorns, and Pegasi in multiple episodes, and several other mythological creatures detailed in individual episode sections below, like manticore, windigo, Hydra, cockatrice, a minotaur, and others.
Rarity's shocked reaction towards Twilight's mane from Friendship is Magic, part 1 is recycled as her excited laugh in Sonic Rainboom.
Fluttershy's nervous squeal from Friendship is Magic, part 1 is re-used three times throughout the series: in A Bird in the Hoof where she is crying over the 'death' of Philomena, again in Hurricane Fluttershy where she is crying under a tree, and in My Little Pony Equestria Girls when her human self gives out fliers to help the animal shelter.
The voice clip of Pinkie Pie's gasp upon meeting Twilight for the first time in Friendship is Magic, part 1, is re-used six times throughout the series: later in the same episode when Rarity confirms that Princess Celestia is missing; in Bridle Gossip, when everyone thinks that they crushed Applejack in the tub; reversed to form Fluttershy's inhalation in Sonic Rainboom; as Mrs. Cake's voice in A Bird in the Hoof, when Pinkie eats Princess Celestia's cupcake; in MMMystery on the Friendship Express, when Pinkie sees that the Marzipan Mascarpone Meringue Madness has been eaten; and in Too Many Pinkie Pies when the Pinkies find out that Twilight's test is watching paint dry. It is reversed again when Pinkie balloons herself in Simple Ways.
In Friendship is Magic, part 2, after Rarity sacrifices her tail for the serpent's moustache, Twilight begins to sympathize for her, beginning with, "Oh, Rarity!" This audio is re-used in A Dog and Pony Show after the team attempts to find an open hole in the ground to save Rarity from the Diamond Dogs.
Pinkie Pie's final line in Friendship is Magic, part 2 is re-used from a line she says in Friendship is Magic, part 1, with some parts cut out during the iris-in.
Pinkie Pie's one-pony band fanfare to rid Ponyville of the parasprites in Swarm of the Century is re-used as the party music in Pinkie's flashback scene in The Cutie Mark Chronicles. Its ending from The Cutie Mark Chronicles is re-used in Sweet and Elite after the first time Pinkie fires her party cannon. The music is used again in A Canterlot Wedding - Part 1 when Pinkie leads Chrysalis disguised as Cadance to her reception plans, and in One Bad Apple for the parade fanfare.
Twilight Sparkle's scream from Winter Wrap Up in the ice skating scene is re-used in Secret of My Excess.
The music that plays during Silver Spoon and Diamond Tiara's cute-ceañera party in Call of the Cutie is the same music that plays during the montage of the Cutie Mark Crusaders' attempts to earn their cutie marks in The Show Stoppers and during Pinkie Pie's birthday party toward the end of Party of One.
The Cutie Mark Crusaders' laughter from Call of the Cutie is re-used in Stare Master when they zoom past Twilight.
Rainbow Dash's laugh in Fall Weather Friends when she flips the sign is re-used again in A Bird in the Hoof.
The background music during Rarity's fashion show in Suited For Success is re-used during Fluttershy's first fashion show in Green Isn't Your Color.
The line 'Holy guacamole!' is spoken by Spike twice in Feeling Pinkie Keen, as is the line "Twitchy tail?."
The musical accompaniment to Rainbow Dash and Rarity's routine in Sonic Rainboom is re-used in The Show Stoppers, when Apple Bloom is practicing dancing; The Cutie Mark Chronicles, during Applejack's flashback; Keep Calm and Flutter On, during the main cast's dinner party with Discord; and Simple Ways during Rarity's first presentation and the Ponyville Days gala.
Rainbow Dash's repetition of "Oh my gosh!" in Sonic Rainboom was re-used again in Wonderbolts Academy.
Most of the background music in Wonderbolts Academy was re-used again in Rainbow Falls.
Fluttershy's laugh that was used twice in Stare Master is re-used in Over a Barrel.
Segments of the Cutie Mark Crusaders' theme song are re-used in My Little Pony Equestria Girls.
Dancing animations for Apple Bloom, Scootaloo, Sweetie Belle, and Twist in Call of the Cutie are re-used in Pinkie Pride for filly versions of Flitter, Cloud Chaser, Lyra Heartstrings, and Sweetie Drops.
Dr. Hooves' descriptions on Enterplay's Mayor Mare & Time Turner trading card, in Gameloft's mobile game, and for Gaia Online's promotional item of him say, to varying effect, that he keeps Ponyville's clocks in sync, sets the hourglass for cider competitions, and takes care of all things "timey-wimey." The phrase "wibbly wobbly, timey wimey stuff" originates from the Doctor Who episode "Blink". In the season five episode Slice of Life and the Korean broadcast of the season one episode Call of the Cutie, Dr. Hooves speaks the phrase "Allons-y!", a signature saying of his live-action counterpart, the 10th Doctor.
The commercial entitled There's a Pony For That is a paraphrase and parody of the Apple commercial There's an App For That, even showing ponified versions of smartphone applications such as Yahoof! and eNay.
The 8 bit commercial features Pinkie Pie playing an 8 bit video game on a console similar to those of Atari, with a controller similar to Nintendo's NES Advantage.
The teaser for season 9, like season 6 before it, also parodies Game of Thrones, which, at the time, was also promoting its final season.
Billboards in Los Angeles, California that promoted the show in June 2011 reference the film Bridesmaids. It shows the main cast against a brick wall in poses similar to the women in the poster of Bridesmaids, under the parody title Bridlemaids.
Billboards for season 2 show Pinkie Pie with her hooves pressed against a "snow screen" TV with the caption "They're baaack!" This references the 1982 supernatural horror movie Poltergeist, which has a poster where the little girl, Carol Anne Freeling, has her hands pressed against a "snow screen" TV and the tagline "They're here" and its 1986 sequel Poltergeist II: The Other Side, which has the tagline "They're back."
On January 8, 2012, a full page ad ran in the LA Times, referencing the opening to AMC's award-winning drama Mad Men. It shows Rainbow Dash in silhouette, wearing a suit, falling in front of pictures of the main cast, with the parody title, Mad Ponies.
Card #PP1 gives the Masked Matter-Horn the secret identity of Trot Summers, a student of Professor Celestia's School for Gifted Youth; these are references to Scott Summers and the X-Men franchise as a whole, respectively.
Card #PP2 describes Mistress Mare-velous as hailing from Alfalfis, a lost city on a hidden island where the female inhabitants are all born with super strength; this is a combined reference to the DC Comics' locations of Atlantis and Themiscyra.
Card #PP3 identifies Radiance as a former pilot named Green Gardener who received her power bracelets from an alien hero; this is an homage to the Green Lantern mythos of DC Comics, with her name specifically referring to Guy Gardner while her origin resembles that of Hal Jordan.
Card #PP4 identifies Fili-Second as Marey Allen, a detective who acquired her super-speed after an accident involving lightning and a chemical plant; these are a parody of Barry Allen's origin story as the Flash.
Card #PP5 details Saddle Rager's backstory: as scientist Spruce Spanner, she was exposed to radiation as a result of an experiment gone wrong, a nod to Bruce Banner's origin story.
Card #PP6 reveals that Zapp is in reality a princess named Aurora who traveled from her distant homeland in disguise to prove herself worthy of becoming queen; this is a nod to the concept of Marvel Comics' Thor.
Collectible card game
Card α #21 R of Gala Appleby has the quote "Sweet Apple Acres is the place for me... Keep Manehattan, just give me that countryside!", a reference to the theme song for Green Acres.
Card α #136 C, Foal Free Press, has the Diamond Tiara quote "I want pictures! Pictures of ponies!", a reference to an internet meme commonly attributed to the Spider-Man character J. Jonah Jameson.
Card #16 R of Pipsqueak has the quote "I wanted a real Red Rider sword for my birthday, but mum said I'd put my eye out", a reference to the 1983 film A Christmas Story.
Card #41 C of Purple Waters has the quote "... and when DJ PON-3 starts spinning different tunes, I'll see the Dark Mare of the moon", a possible reference to Pink Floyd's song "Brain Damage". In fact, Purple Waters' cards contains various references to the former bassist/vocalist of Pink Floyd, Roger Waters. Their names are alike, and Purple has made an album called 'The Fence', parodying the Pink Floyd album 'The Wall'.
Cards #52 and ƒ #21 of Professor Neigh include the quote "Now if you'll excuse me, I have some square roots to calculate. See ya!" This is a play on the closing line of each episode of Bill Nye the Science Guy.
Card #59 U of Top Marks has the quote "He just kept talking in one long, unbroken sentence, moving from topic to topic. It was really quite hypnotic...", paraphrased from a Captain Picard quote in the Star Trek: The Next Generation episode "Timescape".
Card #27 U of Princess Luna has the song lyric "Princess Luna, bring me a dream! Make him the cutest that I've ever seen!", a reference to the Chordettes song "Mr. Sandman".
Cards #75 C and #Pƒ10 of Spike have the quote "Sapphire cupcakes are good, ruby cupcakes are great, but garnet cupcakes are so much better!", a reference to the Cartoon Network animated series Steven Universe.
The Enterplay collectible card game's Twitter account tweeted on August 5, 2015, "Pinkie made malachite cupcakes for Spike once, but they came out all soggy...", a reference to the Steven Universe character Malachite and her extended period of being trapped underwater.
The name of card #138 U, Special Beam Cannon, is the name of a technique used by Piccolo in the anime/manga franchise Dragon Ball.
Card #44 U of Dance Fever has the song lyric "Disco filly, coming through! That filly is you! Ooh ooh! Ooh ooh!", a reference to the Disney Channel original series Gravity Falls and the fictional song "Disco Girl".
Marks in Time
Card #24 R of Discord mentions "an evil interdimensional triangle wearing a tophat", specifically alluding to the Gravity Falls character Bill Cipher.
Card #70 U, Unplanned Guests, Very Animated, has the quote "Oh, it looks like Heero and Duo couldn't make it. They must be busy tonight...", a reference to Heero Yuy and Duo Maxwell of the anime series Mobile Suit Gundam Wing.
Card #87 C, Repulsor Blast, has the quote "All of Princess Celestia's unicorn soldiers are trained in this defensive technique, along with the offensive spell Uni-beam." Repulsor Blast and Unibeam are two techniques used by Iron Man in the Marvel vs. Capcom game series.
Card #93 U, Time Warp, has the quote "Let's NOT do the time warp again, Twilight", referencing the song "Time Warp" from the 1973 rock musical The Rocky Horror Show.
Card #90 U, Hyper Beam, has the Star Swirl the Bearded quote "I am impressed that Starlight Glimmer didn't need a turn to recover after casting that spell!", referencing an effect of the Pokémon move of the same name.
Card #100 U, Tough Questions, has the quote "And how do you become a princess anyway? Strange ponies floating in space distributing wings is no basis for a system of government!", referencing a scene in which King Arthur's right to kingship is questioned in Monty Python and the Holy Grail.
The Master Claw resembles the Master Hand from the Super Smash Bros. video game series.
The in-game description for Bird Whisperer Pony references the song "Feed the Birds" from Disney's Mary Poppins.
The in-game description for Northerly Pony references the film Elf.
The in-game description for Unlucky Pony references the Peanuts franchise, including A Charlie Brown Christmas.
The in-game description for True Umbrum names "H. Pony Lovecart", a parody of H.P. Lovecraft.
The title of the Neigh Anything event "Presentable in Periwinkle" is a play on the 1986 film Pretty in Pink. The community event tasks also feature various 80s musical references:
Prancing in the Dark, a play on Dancing in the Dark.
The Colt 'n' Play, a play on "the Kid 'n Play."
The Robo-Pony, a play on "the robot."
The Safety Prance, a play on Safety Dance
Walk Like a Somnambulan, a play on Walk LIke an Egyptian.
Luna-Walk, a play on the moonwalk.
The Running Mare, a play on the running man.
The in-game description for 8-bit mentions "Hocus Pocus: The Get-Together", a play on Magic: The Gathering.
In the "Cold Front" group quest, Rainbow Dash's line "Make my hay" is a play on the famous line from Dirty Harry.
The character collection name "Elementary, My Dear Stallion" is a reference to the catchphrase often associated with Sherlock Holmes, "Elementary, my dear Watson."
The "Lyra and Bon Bon Save Hearth's Warming" event features quests that are named in parody of various well-known espionage films.
The in-game description for Flawless Rarity refers to her as the "Mare in the Iron Mask", a play on The Man in the Iron Mask.
In "The Las Pegasus Job" group quest, Rarity alludes to Shadow Spade: The Big Sheep, a play on the film The Big Sleep.
In the "Doctor-Shy" group quest, one of Fluttershy's quotes states "It isn't Whoopus, is it...? No...it's never Whoopus...", a reference to the House television series.
The game's adaptation of From the Shadows is entitled "Nightmare Night at the Museum", a play on the Night at the Museum film series.
The bio for Frankenstag's Monster references the following quote from Mary Shelley's Frankenstein: "The fallen angel becomes a malignant devil. Yet even that enemy of God and man had friends and associates in his desolation; I am alone."
The portion of the "Nightmare Night at the Museum" event involving the Marshans references The War of the Worlds by H.G. Wells, who is parodied by the mentioned character H.G. Bales. The bios for Helmeted Marshan and Sniffly Marshan also reference quotes from the work.
The bio for the Cyclops-Clops references a prayer of the cyclops Polyphemous to the Greek god Poseidon in Homer's The Odyssey, with the narrator "Homare" and "Ponysseus" being plays on Homer and Odysseus, respectively.
The bio for Head Chef Pony and an advertisement during the "Royal Dining: Entrée" event mention an Equestrian TV show called Kitchen of Tartarus; this is a play on "Hell's Kitchen" starring Gordon Ramsey, upon whom Head Chef Pony is based.
The Sphinx's riddle from the "Wonderbolt for a Day" event references that from the myth of the sphinx and Oedipus, modified to fit the answer of pony rather than man.
Comments made by Jokester Pinkie during the "Kid's Play" event reference the Joker as depicted in The Dark Knight.
In the same event, Pinkie refers to her "mind palace", a reference to the same concept from the Sherlock television series.
In "The Power Ponies" event, Bat-Mare is mentioned; this is an obvious play on Batman.
Saddle Rager's bio references a quote of Bruce Banner's from the first Marvel's Avengers film.
Cyber Pony's bio references two separate origin stories for the Cybermen of Doctor Who fame.
The in-game descriptions for the various "Resortgoer" ponies reference parodies of real-life Las Vegas hotels, including the Bellagio, Caeser's Palace, the Luxor, Mandalay Bay, the MGM Grand, and Planet Hollywood.
Las Pegasus Singer's bio references two songs by Celine Dion.