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, Cloudchaser, 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.
Twilight mentions "Claw-achella", a reference to the Coachella music festival.
Starlight and Sunburst's use of a drawn circle to "materialize an object that was lost in the past", as well as the ritual's result in failure, mirror the similar plot point of the anime/manga series Fullmetal Alchemist in which lead characters Edward and Alphonse Elric use a Transmutation Circle in an attempt to resurrect their dead mother.
In one of the bubbles of Celestia's dreamscape, Dr. Hooves is seen in a hedge maze avoiding a statue trying to catch him. This is a reference to the Weeping Angels from the sci-fi TV series Doctor Who.
Pinkie Pie's expression "You can lead a yak to water, but you better not let him know you're doing it" is a play on the real-life expression "You can lead a horse to water, but you can't make it drink".
When Pinkie, Rainbow, and A. K. Yearling travel to Somnambula, a map with a moving red line marks their journey, identical to the traveling scenes in the Indiana Jones films—the same allusion to which was made in Daring Don't.
Just as the legends in Campfire Tales were influenced by real-life cultures, the legend of Somnambula draws influences from Ancient Egypt, such as the ponies' clothes and makeup, the pyramids, and the sphinx.
Somnambula shares her name with a G1 villain, a human witch who steals youth from others.
The sphinx's bridge challenge for Somnambula, and Dr. Caballeron's challenge for Daring Do, bears a resemblance to the "Path of God" challenge in Indiana Jones and the Last Crusade.
The title is a play on the expression "a wealth of information".
According to Fluttershy, ancient Equestrian healers like Mage Meadowbrook would wear bird masks to prevent them from getting sick themselves. Twilight and Fluttershy also wore bird masks in the episode to protect themselves from Swamp Fever. This all alludes to the real life medieval Plague doctors who would wear bird shaped masks to prevent infection from the Black Death.
The title alludes to the phrase "once upon a time", a common opening line in fairy tales.
Twilight recalls Shining Armor getting sick on a ride at Pony Island, a reference to Coney Island, a borough of Brooklyn best known for its beaches, boardwalk, and especially its amusement parks Astroland and Luna Park.
Shining Armor does the famous "I'm flying" scene from Titanic while on the airship.
The Neighagra Falls barrel-jumping activity alludes to Annie Edson Taylor, the first woman to survive going over Niagara Falls in a barrel.
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.
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'.
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".
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.