The Elements of Harmony combine to summon the Rainbow of Light. There's even more of a shout out when they're used to beat Discord. Complete with similar music and a World-Healing Wave.
In the Pilot, the ponies have to cross a raging river and a rickety bridge to get to a castle, just like in Rescue from Midnight Castle.
Rarity's butterfly wings in "Sonic Rainboom" and the Glimmer Wings toy ponies are a nod to G1 and G3 winged ponies, the Flutterpony toy line (right down to how they're notorious for having delicate, breakable wings) and the Breezies in particular.
In "The Cutie Mark Chronicles", the younger Fluttershy's thinner body and legs is also reminiscent of the Flutter Ponies. All she's missing are the delicate butterfly wings... which, of course, can be found on her cutie mark instead.
Fluttershy has a yellow coat and pink mane and tail, like Rosedust, Queen of the Flutter Ponies - and her original inspiration Posey (who was an earth pony, but otherwise was nigh-identical in appearance, especially in Lauren Faust's early sketches).
In "Over a Barrel" Spike plays a piano for a show like G1 Spike does in the 1986 My Little Pony Movie.
Discord's mind rape of the mane cast making them lose their color and become jerks is reminiscent of the Smooze from the Original MLP movie, where touching it made a pony act like a jerk and "lose their twinkle".
The design of the Fire Ruby in "Secret Of My Excess" looks exactly like the Heart Stone from the original series episode "Crunch the Rockdog".
Twilight's Twinkling Balloon is actually a shout out to the balloon in MLP G3/G3.5.
Spike sending a photo of the ponies to Princess Celestia at the end of the opening is a reference to the ponies taking a group picture at the end of the G3 and G3.5 openings.
Heck, the opening starts with a shout out to every MLP commercial and theme song ever made.
Applejack is just a redesigned version of the original. She and Spike are the only trademarks that the creators were interested in using that Hasbro retained from the 80s.
Applejack being a cowgirl may come from Megan, the human protagonist from G1 who started off as a Badass Normal cowgirl (though she didn't have an accent or a hat and traded the orange/brown cowgirl outfit for frilly overalls by the time of the Movie).
Applejack's brother Big McIntosh resembles the G3 version of Applejack in color and a cutie mark consisting of just one big apple (as opposed to every other version of Applejack having several smaller apples).
Twilight Sparkle is a fairly direct cross of Powder, Twilight Twinkle and Twilight◊.
Her mother Twilight Velvet, seen in "The Cutie Mark Chronicles" and "A Canterlot Wedding - Part 2" as well as in the Wave 4 Blind Bags, is very clearly based on the G1 Twilight, who was intended to be the original main character of Friendship is Magic.
Her father resembles Nachtlicht, a German-only Pony from G1, a bit too much for comfort. It could be a genderswap Mythology Gag, similar to how Big Mac resembles G3 Applejack. Or just the fact that the name and color scheme fit well into the family theme.
In the first episode Twilight Sparkle gets invited to Moondancer's get-together. This is both a nod to the G1 pony Moondancer and a Development Gag on the fact that Twilight was going to have a variation of Moondancer's cutie marknote It could also be a reference to the G3 Moondancer but considering they're in Canterlot, which is mainly inhabited by Unicorns, it's probably the original Moondancer.
Twilight Sparkle can teleport. In G1, Unicorns can teleport (they call it "winking in" and "winking out"). The first Unicorn seen to teleport is G1 Twilight, in the opening theme of "Rescue from Midnight Castle".
Fluttershy was originally just SUPPOSED to be Posey but Hasbro had lost the trademark on that name.
Her cutie mark however is a shout-out to the G2 Pony Sky Skimmer and her name is based on her Generation 3 incarnation.
Spike being in love with Rarity may be a shout out to G1's Majesty, with whom the original Spike came and Rarity somewhat resembles (although really she's more of an amalgamation of Sparkler◊ and Glory from the G1 line).
Twilight's relationship with Spike mirrors Spike's with Majesty back in G1, especially in the British comics.
Funny enough, Rarity's mannerisms bear resemblance to those of G3 Rainbow Dash, especially her tendency to call everyone "darling".
Early concept sketches of Pinkie Pie were just straight up Surprise◊. Her wings were passed on to Fluttershy and Pinkie Pie was given a swapped version of her G3 color scheme.*
G3 Pinkie Pie had a magenta coat and light pink mane; G4 Pinkie Pie has a light pink coat and magenta mane.
Both Surprise in her original concept and G3 Pinkie Pie have similar cutie marks with 3 balloons. G4 Pinkie Pie's cutie mark is a combination, using the balloon colors (blue and yellow) from G3 Pinkie Pie and the placement of the concept.
The first word out of Pinkie Pie's mouth in the G4 cartoon is "Surprise".
Though it's probably unintentional, Pinkie covered in flour in "Baby Cakes" causes her to resemble Surprise.
Its worth noting that the original Surprise had somewhat greenish blonde hair and Pinkie's mother is white with green hair, though she's not a pegasus.
Twist shares the name with a G1 pony, however it's probably coincidental. G1 Twist was an adult and her Cutie Mark was pretzel related.
The 3rd tier characters Snips and Snails (himself a shout out to the G1 pony Squirmy◊), make up 2/3rds of the ingredients of little boys, the exact opposite of the Sugar, Spice and Everything Nice that created the Powerpuff Girls.
The twin ponies working at the spa are directly based on the twins of the G1 Surprise Twins Pony and/or on the G2 twins Rose and Lily. Both sets were only available in Europe, and Lotus Blossom (the one with the blue coat and pink mane) even has an accent to match!
Most of the large stallions have unshorn fetlocks like the G1 Big Brother Ponies. Two of these large stallions are in fact big brothers, Big McIntosh to Applejack & Apple Bloom and Shining Armor to Twilight Sparkle.
Celestia resembles the G2 Pony design, with a bit of the G1 Beauty Dream Pony thrown in.
Cheerilee had a toy called "Go To School With Cheerilee" which had her as a student in school. Come a few years later and she's a teacher.
Cheerilee was notably requested by Hasbro to appear in the show due to her popularity from G3.
The plot of "The Ticket Master" is near identical to a My Little Pony Tales episode ("And the Winner is..") where one of the ponies wins a pair of tickets to a concert and has to choose which friend to take.
"Dragonshy" is about the ponies climbing a mountain to deal with a dragon in a cave, which also happened in the G3.5 special Twinkle Wish Adventure.
In G3, Spike wakes up from a thousand year nap. In G4, dragons are mentioned to nap for very long, possibly a hundred years or even more.
"Winter Wrap Up" brings to mind the the opening theme to the the 1986 My Little Pony movie:
My Little Pony, My Little Pony All in a twinkling spring is here. My Little Pony, My Little Pony When did all the leaves and grass appear? Where there were snowdrifts, now there are no drifts, Nor is the sky overcast. My Little Pony, My Little Pony Winter is over at last!
In one episode of G1, Wind Whistler had her wings tied during a race, like Rainbow Dash in "Fall Weather Friends".
The foal that Rainbow Dash rescues from the well in "The Mysterious Mare Do Well" has the same body color (and a near-identical voice) as Lickety Split, who had a musical number involving someone else trapped in a well in the original movie.
In "Hearth's Warming Eve" when Rarity (as Princess Platinum) claims Equestria as her own she christens it Unicornia. Unicornia is the name of the unicorns' kingdom from G3 whose princess is named Rarity.
Fluttershy's character in the play is name "Pansy", which almost sounds like "Posey", the G1 pony Fluttershy was base on.
The euphemisms and pony-versions of words characters use come from G1, mainly from European canon. Terms like "Pony feathers!" are the most obvious. Applejack in particular liked to use that term in the British comics, and her G4 Expy often uses it in G4 to.
"The Last Roundup" includes a pony named Cherry Jubilee. There was a G1 pony named Cherries Jubilee.
Party Of One's plot is unusually similar to a comic in the British G1 comics called "A Surprise For Surprise''. In the comic, everypony is ignoring Surprise and telling her to leave them alone. Surprise believes they all hate her and runs off, but it turns out they were throwing a party for Surprise. All the ponies the Mane Cast are based off appear in the strip too.
Flower Wishes, Daisy's name from the toy line, was also the name of a G3 pony.
The stunt that causes Rainbow Dash to crash in "Read It And Weep" is, going by the motions of the onlookers' heads as they follow it, Firefly's trademark double inside-out loop.
"Dragon Quest" has quite a bit in common with the My Little Pony And Friends episode "Spike's Search": They both involve a little purple dragon named Spike leaving behind his pony friends to look for his draconic roots, only to fall in with a crowd of trouble-making dragons, which leads him to decide he's more at home with the ponies.
One of the dragons, Garble, has the same color scheme as Fiery from G1.
In "Hurricane Fluttershy", during the big tornado scene one can see a male pegasus with the color scheme of Firefly, the G1 pegasus who inspired Rainbow Dash.
A pony in "Putting Your Hoof" down - dubbed "Surf" by fans - has a blue mane, pink fur, lightning bolt earrings, and looks like she came right out of The Eighties. She seems to be a Shout Out to Firefly.
When Fluttershy is cleaning during "The Ticket Master", she hums the G1 theme song. It's easy to mistake it for the Friendship is Magic theme tune, since they start the same way, but after the "My Little Pony My Little Pony" part, it clearly follows the melody and beat of the next line of the G1 theme tune ("What will today's adventure be?") rather than the rising "Ah" that follows it in Friendship is Magic, though said beat would eventually find its way into the extended version of the Friendship is Magic theme ("What is friendship all about?")
Might not be intentional, but Princess Platinum's advisor is Clover the Clever. There was a G2 pony named Clever Clover.
In "Applebuck Season", sleep deprivation turns Applejack into a silly pony. Her G1 incarnation was an earth pony forerunner of Derpy (but with apples instead of muffins). A tie-in record was made during G1's run in the UK, one of the songs being the now-memetic "Who's A Silly Pony".
King Sombra is turned to crystal and shattered by the Crystal Heart. G1 villain Lavan was killed when a crystal called the Heart Of Pony Land provided the power needed to shatter him (after he'd already turned to crystal).
He also shares more than a passing resemblance to Tirek who was also killed by exploding.
The advert transition screen from "The Crystal Empire - Part 2" is a large bunch of balloons, which bares a resemblance to the Children's Video Library logo; which is basically the very first thing you see if you play an original VHS copy of Escape from Midnight Castle.
The Crystal Ponies themselves, in their crystal forms, resemble a G1 line with the same appearance called the Sparkle Ponies.
Speaking of Sparkle Ponies, Applejack resembles one when she was covered in glitter in "Apple Family Reunion".
Babs Seed blows her hair out of her eyes like G3's Toola-Roola (incidentally one of only two of G3's Core 7 to not appear in G4 at all; Starsong is the other).
In Sleepless in Ponyville, a mare named Rainbow Dash saves a reckless filly from death by waterfall, like in The Runaway Rainbow.
Other Outside References
Twilight's last name was changed from "Twinkle" to "Sparkle". When Lauren Faust was asked if the name was an intentional joke, her response was "It passed legal."
The Cutie Mark Crusaders are suspiciously similar to the "Pre-Teen Sensations" from Are You There God? It's Me, Margaret., even to the point that they are waiting for a physical transformation and are trying all kinds of irrational stuff to make it happen. The entire scene where they are deciding on a name is almost exactly how it happens in the book.
The first outfit seen in the Costume Test Montage in episode 1 is very clearly the pony version of the Statue of Liberty. In a later episode, we see the statue proper in Manehattan.
Nightmare Moon's exit from her first appearance in the second episode is a shout out to Maleficent's exit in Sleeping Beauty.
Even Applejack holding back Rainbow Dash from charging Nightmare Moon, even though it suits the two of them so well it hasn't been the only time, has a clear parallel in the same scene, with Flora (red fairy) holding back Merryweather (blue).
Nightmare Moon's boasting to Twilight after shattering the elements mirrors a line by Maleficent almost exactly.
Heck, in the beginning of the second episode, they literally take two lines from Sleeping Beauty almost word-for-word.
The manticore has a thorn in its paw. The manticore is part lion. Definitely a shout-out to the fable of Androcles and the Lion.
The part of the manticore scene where Rainbow Dash attempts to create a vortex around the beast is very similar to a battle in BIONICLE where Lewa Nuva attempted the same move against the Rahi Nui (Which is more or less a biomechanical manticore). In both stories, the creature sticks a limb into its enemy's path and sends them sprawling.
Luna is given a wreath of red and white roses, referring to the Tudor crest used to symbolize peace after the War of the Roses.
"Ticket Master" includes a Benny Hill-style chase scene, right down to a Suspiciously Similar version of "Yakkity Sax" playing in the background. Like the original, this BGM has been reused for every wacky chase scene throughout the show, twice so far (although the second one is slightly different and actually even closer to the original).
The same episode includes Snips and Snails making a Pinky and the Brain reference, and when Rarity demands for a mirror to see the mess Trixie made to her mane, she is mimicking The Joker's mirror scene from Tim Burton's first Batman movie.
The shout out to Batman is even more powerful when you realize Rarity is wearing a purple dress, her face is white and her hair is, well, green.
In "Dragonshy", the music that plays during the preparation montage – as well as the montage itself – is a combination of references to The A-Team and Charlie's Angels. Additionally, the music that plays during the girls' journey up the mountain is a variation on the theme for The Lord of the Rings.
The Lord of the Rings music takes on an especially humorous light seeing as the dragon's design from that episode seems to be based on Smaug.
Rarity seals herself in her bedroom, shouting "I vant to be alone!" She does it again in "Green Isn't Your Color".
During the second fashion show, the background music features multiple shout-outs. In the beginning and end, the music takes cues from "Also Sprach Zarathustra". Pinkie Pie's segment takes cues from both I Want Candy by Bow Wow Wow and the Cartoon Cartoon music from Cartoon Network. Fluttershy's segment is based off of Claude Debussy's L'après-midi d'un faune
The entire sequence where Twilight was stalking Pinkie in "Feeling Pinkie Keen" took multiple aspects from Roadrunner and Wile E. Coyote, including gag scientific names, as well as Anvil On Head and Piano Drop.
Early on, Twilight asks Pinkie Pie "What in the wide wide world of Equestria are you up to?", another reference to Blazing Saddles (the original line in the film was "What in the wide wide world of sports...", a reference to the popular ABC television show of the same name).
The "Pinkie Sense" itself is a nod to Spiderman's Spidey Sense.
The swirling blue "whirlpool" accompanying Rarity's transformation in "Sonic Rainboom" is a reference to The Swan Princess.
What happens to Rarity's wings at the end of the episode is a direct reference to the Greek myth of Icarus.
In "Stare Master", Sweetie Belle makes the comment "who wants a hammer on their flank anyway". As a matter of fact, the Wreckers, the Autobot subgroup from Hasbro's other major property Transformers, have a hammer over their usual Autobot symbols.
On top of that, in "The Super Speedy Cider Squeezy 6000", there's a background pony with a hammer and a lightning bolt. on her flank
In "The Show Stoppers", Scootaloo's failure to find a decent rhyme, frustrated "NEVER, NEVER!", and piano head-desking are lifted straight from Don Music in Sesame Street.note A character who was dropped because of concerns that children were imitating this behavior.
The outfits worn by the Cutie Mark Crusaders for the talent show make them look like the Misfits from Jem (another famous girls' cartoon from The Eighties).
The So Bad, It's Good style of the CMC's Theme Song is also a shout out to the Misfits' musical style, that is off-key screaming metal of the 80s, a la KISS.
The way the Cutie Mark Crusaders are lit when their song begins is an obvious shout-out to the music video for Queen's Bohemian Rhapsody◊.
The audience's reaction to the performance and its unintentional hilarity is almost directly lifted from The Producers.
In "A Dog and Pony Show", the diamond dogs themselves speak in a manner similar to Gollum from The Lord of the Rings films, have a gangly appearance similar to Gollum, and even refer to the gems as "precious".
The name "Diamond Dogs" has got to be a shout out to the David Bowie album. The title song from that album contains the line "The diamond dogs are poachers, and they hide behind trees". When we first see the dogs, they are hiding in a tree and planning to steal the gems Rarity and Spike are collecting.
In the cold open, the music is reminiscent of The Legend of Zelda games while Rarity places rupee-shaped gems on her latest dress. The blue one even flies up from an open chest, much like those found in the games. In a related shout-out to Zelda, the Diamond Dogs are similar in shape to Moblins.
The music that plays when the girls try to get into the rapidly filling holes takes a few cues from the Rite Of Spring.
At one point, one of the dogs keeps popping up from different holes while Applejack is trying to catch him, while a soundeffect straight from a Whack-A-Mole machine plays.
The leader of the Diamond Dogs wears a red vest just like the Grundle King's from the 1986 movie.
In "Over a Barrel", when Spike walks off in a huff because the girls keep interrupting his sleep, Fluttershy calls him "Huffy the Magic Dragon". Made all the more bizarre by the fact that Fluttershy says it as if she's deliberately making the reference, and Twilight seems to get the joke. This is immediately followed by a gag used in The Emperor's New Groove – Rarity getting up angrily and scaring the others with her Cucumber Facial.
The climactic slapstick pie fight near the end of the episode is almost certainly a Blazing Saddles reference.
This episode makes at least two shout-outs to the classic Bugs Bunny short "Bully For Bugs": both the buffalo from this episode and the bull from the Bugs Bunny cartoon sharpen their horns using a grinding wheel, and the buffalo running into an anvil hidden in a hay bale mirrors the bull running into an anvil hidden behind Bugs' red muleta.
The scene where the buffalo line up along the edge of the cliff before charging down towards the town is a reference to a Tex Avery short to boot.
There are a couple widescreen closeup shots of the Buffalo chief's eyes that are very Leone-esque.
The name of the apple tree Applejack is tending to is named Bloomberg. The mayor of New York City (a.k.a "The Big Apple") at the time of the episode's airing is Michael Bloomberg.
At one point before the big battle is about to begin, Rainbow Dash tries to think of something in a manner reminiscent of Winnie the Pooh, tapping her hoof to her head repeating "think" to herself.
The overall plot of the episode is reminiscent of the scene in Harry Potter and the Chamber of Secrets where Dumbledore's pet bird burns to ash in front of Harry, and Harry thinks he's in deep trouble until Dumbledore reveals that his pet is a phoenix. Philomena even looks a fair deal like almost dead Fawkes.
Drilled in when Princess Celestia cheerfully states "lovely, isn't she?" and is still quite cheerful when everyone else is horrified, and is clearly enjoying having fun with the other ponies, Dumbledore-style. She even urges on Philomeena to quit milking the melodrama and rebirth already, just like Dumbledore.
And during Celestia's brunch at the Sugarcube Corner, right when she announces that she must leave because royal duty is calling, the scene looks very similar to "The Last Supper" from Leonardo da Vinci. (Even the number of ponies on screen is exactly twelve and Celestia makes it 13.)
The little green hummingbird Fluttershy brings in as a friend for Philomena is "Hummingway".
This is followed by another instance of Fluttershy (and Hummingway) singing a tune similar to the theme song.
In "Green Isn't Your Color", one of the photos of Fluttershy shows her in Eeyore's signature slump.
"The Cutie Mark Chronicles" had a scene where Filly Applejack watches a pony version of the Statue of Liberty (linking back to Twilight's outfit in the pilot).
Filly Rarity also (literally) bumps into a rock that resembles the black monolith from 2001: A Space Odyssey, musical fanfare included.
This part also brings to mind the scene in The Road to El Dorado in which the main duo also come before a great big rock (Rarity's complaints about it have a similar tone to Tulio's) after thinking that it led to their main goal (which in both cases, turns out to be true).
Filly Twilight Sparkle tries to get accepted into "Princess Celestia's School For Gifted Unicorns" and during the admission exam her magical power violently awakens, turning her into a huge danger for everyone and herself, until Princess Celestia herself manages to calm her down and offers herself as her guide so she could learn how to control her immense magical power. The entire scene is a shout out to X-Men, with Twilight as Jean Grey, Celestia as Charles Xavier and the school itself a shout-out to "Xavier's School for Gifted Youngsters".
"There was no talking. There was no smiling. There were only rocks." Think that type of dystopian narration sounds a bit familiar?
Filly Fluttershy's song really seems to hearken back to the various Disney princess movies.
When Spike's looking for a new quill, one of the places he looks is in the shower, where Owlowiscious happens to be bathing. This is likely a reference to the Jean Craighead George book There's an Owl in the Shower.
The whole episode may be a reference to the 1970 The Pink Panther short Muff The Magic Dragon.
When Spike first sees him, Owlowiscious is looking outside and to look at Spike, his head does a 180° while the lightning darkens and a scary tune plays. As Spike comments "Dude, that's creepy."
The opening of "The Best Night Ever" has Twilight channeling the Fairy Godmother by making a carriage out of an apple and horses out of mice, even adding the stipulation that they'll revert by midnight. The ending also includes a bit about one of Rarity's glass slippers.
Of course, after seeing how much of a douche her dream prince actually is, she destroys the slipper, not wanting him to find her.
Discord also "Force Chokes" the Mane Cast during the final confrontation.
One background pony making her debut in this episode has a screw and a baseball for a cutie mark. In older cartoons, such as the Daffy Duck short "Duck Amuck", this was the universal sign for "screwball"
The whole of Discorded Ponyville, especially during Twilight's sorrowful walk back to the library after being Discorded herself, seems to be an homage to Wackyland.
After Applejack and Apple Bloom drive sheep into a corral, one of the sheep says "You could have just asked," referencing a scene from Babe.
In the bowling alley scene at the start of "The Cutie Pox", you can see pony versions of several characters from The Big Lebowski, including Jesus Quintana, Walter Sobchak, Donny, and the Dude.
Two of them were later named in a licensed mobile game by Gameloft: Jeff "The Dude" Letrotski and Jesús Pezuña. The pony resembling Walter was added to the same game for a winter update, but he was called simply "Bowling Pony".
One shot inside the Apple family's house features a painting in the background that looks like a pony version of Grant Wood's American Gothic.
The statue that Apple Bloom carve is a direct reference to the Renaissance Italian painting The Birth of Venus.
After a chess-playing cutie mark appears on her, Apple Bloom plays, and beats, a chess-playing pony who looks an awful lot like Geri.
Apple Bloom first discovers she's forced to use the talents the Cutie Pox gives her with a tap dancing mark, referring to the Hans Christian Anderson story "The Red Shoes".
The part where Apple Bloom is diagnosed is awfully reminiscent of a typical House scene, team and everything.
In "May The Best Pet Win!", Rainbow Dash's wing becoming trapped beneath a bolder in a canyon is reminiscent of hiker Aron Ralston, who was trapped in a canyon for five days when a falling bolder pinned his arm.
After first failing to supply Dash's need for an awesome pet with a bunny, the next thing she brings out is a "puddy tat".
Rainbow Dash's first attempt to stop the runaway coach resembles Peter Parker's first attempt at stopping the elevated subway in Spider-Man 2.
The crane driver is an earth pony version of the pegasus foreman from "Feeling Pinkie Keen", who might look like Fred Flintstone.
In "Sweet and Elite", a painting in an art gallery is inspired by Salvador Dali's Persistence of Memory.
Twilight's awkward dancing at the Canterlot ponies' party mirrors a scene in Seinfeld.
The underscore as Rarity soaks Opal in water is a reference to Ravel's famous piece "Bolero".
The design of the blimp that Rarity helps see off in her musical number evokes the Wind Fish.
The overworked bellhop pony seems to be based on the Squeaky Voiced Teen from The Simpsons.
The music in the cold open of "Secret of My Excess" is inspired by The Sorcerer's Apprentice. This music recurs several times throughout the episode, including a sequence when Twilight lures Spike back to the library by baiting him with a broomstick.
The re-shelving scene seems slightly similiar to this scene.
In addition to King Kong references above, the presence of a giant rampaging lizard has a tendency to make one think of Godzilla. His roar is almost directly lifted from that franchise.
The scene where Rarity's tears fly upward as she and Spike free-fall seems reminiscent of Spirited Away.
Twilight teleporting Spike back to her to clean his cheek, yet another allusion to Doctor Who.
Spike's monstrous corruption after greedily demanding extra birthday presents is similar to the fall of Smeagol.
Applejack's line "Twilight, get my rope" isareferenceto a Pace Picante sauce commercial from the '80s.
In Family Appreciation Day, Apple Bloom gets called "Half Pint" when wearing the same bonnet Laura "Half Pint" Ingalls wore.
At the very beginning of the episode, Granny Smith is running around in the middle of the night causing a huge ruckus in direct reference to the famous Midnight Ride of Paul Revere.
The scene in "Baby Cakes" where Pinkie suddenly sees Pound Cake walking along the ceiling may be a nod to, of all things, the film version of Trainspotting.
Cranky's snowglobe in "A Friend In Deed" is clearly based on the one from the infamous final episode of St. Elsewhere.
One of Pinkie's guesses as to what the "C" in C.D.D. stands for is "Chico".
Cranky's name and species, as well as the ending music, are a giant reference to the song Yankee Doodle, particularly the first verses.
The music that accompanies Iron Will's first appearance in "Putting Your Hoof Down" is a play on Eye of the Tiger from the Rocky movies.
The music that plays when Fluttershy realizes her assertiveness has gone too far is almost exactly like The Lonely Man from the The Incredible Hulk. What is more, it plays as Fluttershy walks down a road slowly, away from the camera.
The music playing during her conversation with herself (both in the beginning of the episode, and when the same scene is revisited at the end) is a remix of "I am the Doctor", a piece of Doctor Who music. Also, Future Twilight's appearance is preceded by a sound similar to the one heard when the TARDIS materializes. (A key being rubbed against a piano string, incidentally.)
When Twilight, Pinkie and Spike circle around to where they started while sneaking around the Canterlot Archives, Spike says "Isn't this where we came in?"
Citizen Tiara, anypony? Diamond Tiara addresses the rest of the students from behind a podium in front of a giant-sized portrait of herself, and turns the Foal Free Press into a success based on yellow journalism. Fortunately for her, she's still young enough to avoid Kane's Downer Ending and learn from her mistakes... maybe.
Her scenes also contain nods to John Jonah Jameson of the Daily Bungle from Spiderman.
"MMMMystery On The Friendship Express is direct homage to Murder on the Orient Express, and borrows several plot elements, including the ending.
Donut Joe's antics as Pinkie imagines them are based off the James Bond series of films. Gustave is portrayed as a Dastardly Whiplash-type villain, and Mulia is portrayed as a Kurosawa-esque ninja.
Andrew Francis is a captain of the guard, Kathleen Barr voices an evil queen commanding a legion of insectlike creatures... seems familiar...
The Changeling Queen's plot to take over Canterlot is similar to Ursula's plot to take over the sea in The Little Mermaid. Both disguise themselves as the bride, both possess the bridegroom, and both get a Villain Song where they sing about their plans into a mirror!
The end of the fight scene between the Changelings and the Mane 6 resembles that of one of the shows Lauren previously worked on.
The way Shining Armor's shield looks and works is quite reminiscent of the shield that was put up to protect Hogwarts in Harry Potter and the Deathly Hallows, Part 2.
When impostor Cadance is singing her half of the duet, we see the chandelier in her chamber—straight out of the Myst library.
In the preview clip for "The Crystal Empire", Pinkie Pie's night-vision goggles look a lot like the ones worn by Sam Fisher, only in gold and yellow. Also, when Pinkie startles two of the Crystal Ponies, when she says "A spy?! How did they know?!", if you listen carefully you can hear a very slight musical cue that sounds awfully similar to the James Bond theme.
The first episode deals with a magical kingdom that has a powerful device/object that is hold sacred by its inhabitants. Suddenly, an evil man/creature tries to seize this power to himself and ultimately corrupts the land because of his evil heart, turning it into a wasteland and the castle into his tower, leading the goddesses to seal him away only to return after many years and try to seize this power once again. Gee, where have I heard this before?
The scene where the crystal heart returns and protects the city is similar to the ending of Atlantis: The Lost Empire, right down to the magic forcefield.
The whole plot actually shares a lot of elements from Atlantis. The city's general layout, the fact it was lost for a long time, amnesiac citizens, a missing page in the otherwise complete guidebook to the civilization, which details how the power crystal which protects the empire works. Uh huh. Totally a coincidence.
Shining Armor's appearance when he arrives at the station may pretty well be the Star WarsShout Out one can find in every season opener.
Twilight's training with Zecora in "Magic Duel" shares some similarities with the one Luke once went through, taking place in the local lost woods of sorts, having a mentor who puts a lot of emphasis on concentration and likes to talk funny, down to the training itself involving levitating objects while standing on water - and failing due to similar distractions. Not to mention that Trixie's dark cloak and red magic aura make her look very much like a Sith Lord.
The Mayor being stuck in a cage in the center of the town surrounded by evil brings Deckard Cain to the minds of many viewers.
In Sleepless in Ponyville, the scene where Scootaloo tries to run away from the Headless Horse is reminiscent of the last part of Disney's The Legend of Sleepy Hollow and the final shot of Scootaloo and Rainbow Dash flying is similar to the final shots of the Superman movies.
The mustached instructor pegasus accompanying Spitfire very closely resembles a pony version of Viper from Top Gun.
Pinkie's subplot with the mailbox brings to mind an episode from another show Merriwether Williams wrote for.
Pinkie Pie appearing right behind the other ponies while they were still watching her from a distance could be seen as a nod to Dio Brandowho was able to move and appear great distances while people's eyes were still trained on him, or even move victims.
Even though, the roles of protagonist and The Rival (and loyal second) are inverted from Top Gun, and Lightning Dust's attitude toward team flying is more like Maverick, her mane nonetheless bears a more than passing resemblance to Iceman's haircut.
One of Spitfire's uniform badges closely resembles the rank insignia from the Star Trek: The Next Generation episode "Future Imperfect", while the three red pips underneath it are very reminiscent of the stars worn by Royal Manticoran Navy officers to denote their previous hyperspace-capable starship commands.
"Magical Mystery Cure": In the opening musical number two stallions lift Twilight down from a table where she was dancing and she runs forward. It's very reminiscent of the big dance scene at the end of Dirty Dancing.
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Rainbow Dash's idols, the Wonderbolts aerobatic flight team, appear to be named after the Thunderbirds, while their blue-and-yellow outfits are likely a reference to the Blue Angels.
Similarly, the Shadowbolts' logo resembles the logo of the Hells' Angels.
Hoity Toity is a clone of German designer Karl Lagerfeld.
Photo Finish is Vogue editor Anna Wintour.
The manly tennis player pony ("Ace") in "Call of the Cutie" and "Luna Eclipsed" is based on Andre Agassi.
The backstage manager at the Best Young Flyer competition ("Lucy") in "Sonic Rainboom" who later appears as a unicorn with a different cutie mark in "Putting Your Hoof Down" is based on Lucille Ball.
Mulia Mild's name, career, and voice are all based on Julia Child.
The Royal Wedding of Shining Armor and Princess Cadance is a shout out to the wedding of Prince William and Kate Middleton, down to the red shirt and blue sash that Shining Armor wears and the timing of the episode (close to Will and Kate's 1st anniversary).
In episode "Putting Your Hoof Down", the motivational speaker (and minotaur) Iron Will is voice-acted to mimic and parody Anthony Robbins, life coach and motivational speaker.
One of the background characters (eventually dubbed "Time Turner" by the company) is based on David Tennant's portrayal of Doctor Who. A few of his appearances (and one of his collectible cards) directly reference lines from episodes in which Tennant played the Doctor.
Oddly enough, expies of the Doctor as portrayed by John Pertwee, Peter Davidson, and Matt Smith have also appeared in-show, and they have the same cutie mark as Time Turner.
Even the advertising for the show gets in on this.
Narrator: Without them the Grand Galloping Gala would be neither Grand nor Galloping. They are The Most Interesting Ponies in the World. Pinkie Pie:(in a Spanish accent) I don't always watch tv, but when I do, I prefer My Little Pony: Friendship is Magic. Twilight Sparkle: Stay pony, my friends.
The officially licensed shirts and bags have a lot of shout outs. This shirt is inspired by illustrator Hajime Sorayama, and may also be a reference to something else. It should be noted, however, that the shirts by We Love Fine are not designed in-house by Hasbro, but instead by designers who specialize in pop culture, as well as featuring contest-winning designs submitted by fans.
Pretty much any town or city mentioned in the show and/or shirts other than Ponyville is a direct reference to some location from real life. Canterlot is based on Camelot and Canterbury, Fillydelphia on Philadelphia, and so on.
So that would make Ponyville based on Townsville?
Possible, but not likely, as the G3 version was also centered around a town named Ponyville. While PPG is older than MLP G3/3.5, Lauren Faust was working on another show at the time of the G3 animation productions.
She has also stated that her original idea was to call the central village Fillydelphia, but Hasbro insisted on Ponyville.
In the Season 2 finale, Spike is shown playing with wedding cake figures of Princess Cadance and Shining Armor. Guess which two ponies are going to be in an upcoming play set together?
A poster◊ that showed up at Hasbro's booth at a licensing expo was adorned with, in familiar writing, the caption of This is Vın̈yl Scratch.