Hurricane Fluttershy

• In the opening scene, Fluttershy tries to avoid going to the Pegasus meeting by disguising herself as a tree. This is likely a reference to her famous line from Over a Barrel, "I'd like to be a tree", which has become an in-joke in the fan community.​[​citation needed​]​
• Fluttershy's training montage features music very similar to Joe Esposito's "You're the Best", as featured in the 1984 film The Karate Kid.

Ponyville Confidential

• The title of the episode is an allusion to James Ellroy's 1990 novel L.A. Confidential and the 1997 film adaptation. The episode's theme is a reference to its Hush Hush Magazine subplot.
• Diamond Tiara's drive to make the paper successful by any means necessary is similar to the rise of Charles Foster Kane in the movie Citizen Kane. Her introductory speech in front of a large portrait of herself is inspired by the scene of Kane's campaign speech.
• The headline "Snips and Snails and Bubblegum Fails" is an allusion to the nursery rhyme "What Are Little Boys Made Of?".
• Rarity's line "Et tu, Gabby Gums?" is an allusion to the Latin phrase "Et tu, Brute?", traditionally attributed to Julius Caesar's last words in the Shakespeare play of the same name, and is meant to express great shock against a trusted one's betrayal.
• "Gabby Gums'" line "XOXO, Gabby Gums" is an allusion to the book and TV series "Gossip Girl", where the voice of the character always signs out with the phrase "XOXO, Gossip Girl".
• One of Apple Bloom's baby photos is posed the same as the Coppertone girl ad.
• Ponyville's newspaper, The Ponyville Express, is similar in name to the Pony Express, a famous mail service used in 1860 and 1861 in the United States.
• The headline "Fluttershy Has Tail Extensions" references the real-life practice of hair extensions.
• Pinkie Pie's reaction to the headline "Pinkie Pie is an Out-of-Control Party Animal" is reminiscent of the classic dramatic archetype of an addict breaking down and admitting that they have an addiction.

MMMystery on the Friendship Express

• The title of the episode references the 1934 crime novel Murder on the Orient Express by Agatha Christie, as does the outcome of the case: nearly every passenger is responsible for one part of the "crime".
• The hat Pinkie Pie wears and the bubble-blowing pipe are references to the fictional detective Sherlock Holmes. Twilight's hat also resembles that of John Watson, Sherlock's partner.
• One of the books sticking out of Twilight's bag in her first appearance in the episode is the history book from the beginning of "Friendship is Magic, Part 1."
• When describing the cake, Pinkie Pie references the Cole Porter song "It's De-Lovely."
• Mulia Mild's name and mannerisms are a reference to Julia Child.
• Pinkie's fantasies of the other bakers during her accusations are all allusions to multiple styles and genres of film:
  • First, the Gustave le Grand fantasy references black and white silent films, with Gustave playing the role of the dastardly villain often associated with films from the period. The vignette may also be a specific nod to Snidely Whiplash, himself an animated parody of over-the-top silent film villains (antagonist of Dudley Do-Right of the Mounties segments on The Rocky and Bullwinkle Show).
  • Donut Joe's persona in Pinkie's fantasy, "Con Mane", is a reference to fictional secret agent, James Bond; additionally, the opening to this fantasy parodies the franchise's iconic gun barrel sequence.
  • Finally, Pinkie's fantasy about Mulia destroying the cake is a reference to the Japanese film Yojimbo and similar ninja genre films.
• At one point Pinkie Pie says she wants to know "who done it" before Twilight Sparkle pedantically corrects her grammar. The type of mystery being spoofed in this episode is known as a "Whodunnit" as opposed to a "How Catch 'Em" or "Procedural".
• The episode also references the 1943 film I Dood It, starring Red Skelton.