Due to the rapidly expanding nature of the universe, and it's status as a Crossover of My Little Pony: Friendship Is Magic with the Marvel Universe, Shout-Outs abound, either as direct references to other characters within the Marvel Universe or other, non-Marvel references, with everything from Pink Floyd to The Bible being referenced in one form or another.
Phase One of the Harmony's Warriors universe acts as both the first wave of stories and functions to act as a foundation for subsequent stories. It focuses almost exclusively on the Mane Six and their origins as superheroes.
These are the shout-outs contained in those stories.
- The first half of Rarity's dream in Chapter 6 definitely has a Cowboy Bebop feel to it:Frog: Didn't ya hear me? You're on a stairway to heaven!
Rarity: Don't you know you're one heck of an annoying frog?
Frog: Fine. Be that way. But don't say I didn't warn ya...
- Bruce Mane is shown at a party drinking ginger ale. And his one line of dialogue is lifted directly from Batman Begins.Bruce Mane: A pony who dresses up as a bat clearly has issues.
- Similarly, Carmel Apple, a background pony, shows up as a reporter at Rarity's press conference. According to the writer's blog posts, Carmel is this universe's version of Clark Kent.
- Also, at a science conference at the beginning of the story, Bon-Bon appears (under the name "Sweetie Drops", her Hasbro-given name), and is described as a biochemist. She is intended to become this universe's version of Ant-Man. Another attendee is Dr. Whooves (here called Time Turner), who is accompanied by a grey mare with a blond mane; this is almost certainly Derpy Hooves. These two will reportedly eventually become this universe's Mr. Fantastic and Invisible Woman.
- When designing her armor, Rarity makes a comment about needing to Reverse the Polarity, in a direct shout out to the Third Doctor.
- Sweetie Belle's middle name is Lauren.
- Sweetie Belle is also a fan of anime like Inuyasha and Neon Genesis Evangelion.
- There are several when Rarity is flipping through channels, like "Girl, why you ackin so cray cray?".
- Ishval serves as the story's Afghanistan stand-in.
- Two terrorists are named for Roman Polanski and Xavier Dolan.
- The street gang that assaults Fluttershy early on is a clear shout out to A Clockwork Orange.
- The gang of griffins who get killed by Gilda are named Roger, Nick, Rick, Syd and Dave, which are the first names of the band members of Pink Floyd.
- Speaking of, there are several Marvel cameos in this story. Gilda the griffin is Wolverine and gets into a bar fight, and Zecora saves Fluttershy from a timber wolf and takes her in for a chapter or two, but she is secretly the Black Panther. Babs Apple is Rogue, a future X-Man, and meets Fluttershy on the subway, and Cherilee is Dr. Curt Conners aka the Lizard, a future Spider-Man villain who tries to help cure Fluttershy.
- The griffin motel owner/part time artist that Fluttershy meets is named after political cartoonist Gerald Scarfe.
- Fluttershy and Hoofcuff's encounter in the sewers is quite similar to the one between Kimble and Gerard in The Fugitive.
- Pony versions of Sam and Dean show up in the epilogue as N.E.I.G.H. agents interviewing Hoofcuff about the events of the story.
- A pony (who is not explicitly named but fits the description of Mjolna) shows up in the first diner scene and mimics Rainbow Dash's action of smashing her mug against the floor. The character is intended to eventually become Beta Ray Bill, a Thor supporting character.
- When Rainbow Dash is captured by N.E.I.G.H., she's interrogated by a detective named Fetlock and his assistant Trotson, the former of whom can tell nearly everything about her just by looking.
- A donkey version of William Shatner (named Tiberius) cameos in one chapter as a diner owner.
- A local chain of grocery stores is named Firth of Fifth
- Rainbow's father, Siegfried, is named after the hero of the Wagner's opera Siegfried
- Trixie's nightmare was based off the dinner scene from Shakespeare's Macbeth
- The village that a young Carrot Cake lives in at the beginning of the story is named "Prospekt", which is a reference to an EP by the band Coldplay
- One of Gustav's soldiers is named Fassbender, after Micheal Fassbender, the actor who played Magneto in X-Men: First Class.
- One of the survalience reports on Carrot Cake is written by an agent whose number is "24601", which is Jean Valjean's prison number in Les Misérables.
- When Carrot calls out Gustav on killing his mother, Gustav replies "I killed my mother too, but you don't hear me whining and crying about it."
- The dragon village that Carrot goes to in order to look for some of Gustav's former employees is named after Smaug.
- The scene where Twilight interrogates one of Gustav's minions is based on the opening of Zero Dark Thirty.
- At one point, Spike and Strong Hoof argue over which is the better sci-fi show, To Boldly Go or Adventures in Time and Space.
- Daring Do's father, the history professor at Canterlot University (where Cupcake attends), is named Professor Jones (fitting, since Daring is viewed as a pony expy of Indy).
Phase Two of the universe focuses on characters outside of the Mane Six, and builds on events that occurred in Phase One.
- Two of the scientists sent to find the spider are named Bunsen and Honeydew (although Bunsen calls him Beaker)
- Honeydew apparently once spent some time as an Energy Being after leaving his father's watch in a field subtraction chamber and getting zapped.
- During Diamond Tiara's Power Incontinence freak-out, one of the thoughts she hears concerns a pony named Tiberius facing off against the Gorn.
- The Baxter Building equivalent is called The Tardis Tower.
- Pip's science teacher is Ms. Frizzle (Word of God is that she's the same Ms. Frizzle that appeared in Captain Equestria, and that she's a Time Lady), and their Principal is named Wakleflanks.
- Pip and Dinky are big science fiction fans in this universe, and during their first real conversation in chapter 2 they discuss the local versions Doctor Who (with the series title coming from An Adventure in Space and Time), Star Trek, called To Boldly Go (which is another fic by the same author), and Back to the Future.
- Berry Punch mentions having to work a job in Gravity Falls after dropping her daughter off at Cheerilee's.
- Featherweight makes a reference to the pony version of the Canadian horror director David Cronenberg.
- A-H says that Mrs. Barometer would be voiced by the late voice actor who voiced The Witch of the Waste.
Due to the projected size of the Harmony's Warriors universe, side stories are frequently used to help fill in the gaps and tell a story that otherwise might not be enough to carry an entire full length story. So far, there is only one side story, but more are planned.
These are the shout-outs contained in those stories.
- When Pinkie is first given her assignment, she's hoping it's a golden ticket to the candy factory she's heard of.
- Pinkie apparently once had an encounter with the Doctor, who apparently tried to drag them off to the 23rd century. And he gave her his sonic screwdriver.
- We have Lin Beifong as a senator that Pinkie and her sister Marble are instructed to look after.
- Lin uses a soul gaze on Pinkie when she finds out about Pinkamena.