- In the Silverfish Arc there is a fish with legs.
- "What Big Teeth" opens with Sweetheart in Joe Cool style dark glasses narrating "Here stands the director of Project Skin Horse..."
- A number to The Wonderful Wizard of Oz and its sequels, as seen in arc titles like "Cowardly Lion". A list of the characters who are shout outs to Oz books would include almost all of them.
- Nick Zerhakker deserves special mention—in addition to his last name sounding like "the hacker," which he sorta is, and actually translating to "helicopter" or "chopper," which he definitely is, it is also a reference to "Nick Chopper"—the Tin Woodman's real name.
- Unity's sewed together appearance and personality are a weaponized version of the lesser known character and sometime love interest for the better known scarecrow, The Patchwork Girl of Oz. First seen in... The Patchwork Girl of Oz.
- Tip is the name of Ozma when she was in the form of a boy in The Marvelous Land of Oz.
- Moustachio the aged robot receptionist is a lot like Tik-Tok the clockwork man.
- The Department of Irradiation wears green goggles.
- Goldbug shatters Nick's virtual world with a direct quote from the Wizard. Later Gavotte calls Goldbug "You great humbug". Goldbug's real identity is foreshadowed by stealth Wizard of Oz references stretching back to the beginning of the strip.
- The Hungry Tiger gets a nod with H.T., co-creator of "AsLAN".
- As of "Looking Glass Land", Skin Horse is based in the Maragda Building. "Maragda" is Catalan for "emerald".
- Tip has a psych book called Everything but Live: Creating a Therapeutic Environment for Nontraditional Intelligences. The advertisement card on Tik-Tok's back declared he "Thinks, Speaks, Acts, and Does Everything but Live".
- In "Fun for Some", Nick's fellow playtester (and female mind-copy) is named Aimee. The girl the Tin Woodsman was in love with before he lost his heart was named Nimee Amee.
- Unity's car has a bumper sticker that says "Rocket Nixon 2008". This is a reference to the webcomic "The Chronicles of William Bazillion", which is drawn by Shaenon K. Garrity's husband.
- Shout-outs to both The Big Lebowski and Interstellar Pig in the same strip.
- Gavotte the leader, is the one who drinks the tea in homage to Esmerelda Weatherwax.
- The fact that she's a swarm of bees helps here...
- She's also a bit Mary Poppins, in particular using the phrase "spit-spot".
- They borrow a Flying Machine from Wendy of the Department of Jetpack Surpression.
- Perhaps a slight stretch, but we also have Gerda, who works in Cryonics.
- Chris shows up wearing an xkcd t-shirt.
- This strip has a quick one to Andrew Marvell's "To His Coy Mistress": Cypress is said to "grow vaster than empires and very quickly."
- Unity just had to make at least one Frankenstein (1931) movie reference. In this case, "Fire...bad?"
- "Choose" has a number of references to Spider and Web, starting here
- As mentioned earlier, "Choose" is a send-up of the Choose Your Own Adventure series - including tiny details like the exact same font the original book series used every single onscreen time Jonah gets "The End."
- Nera is named for a recurring character from that series, Nera Vivaldi, and Jonah is likely named for the CYOA book "Your Code Name is Jonah," which is fitting since he's the one experiencing the many endings. Jonah's surname, Yu, is a punny reference to the main character in the books being "you".
- Slaughterhouse-Five also comes up occasionally - the Department of Precambrian Defense is unstuck in time, and "Choose" marks its first The End with a little bird going "poo-tee-weet!"
- When Nick arrives to rescue Tip and Sweetheart from zombies with a massive tree-trimming attachment on his chassis, he naturally describes it as "Groovy".
- "Railway Children" features a Mad Scientist city that exists as a giant subway train underneath Boston. "Welcome to St. Charlie, the city that never returns!"
- G.O.D.O.T., the Genetic Organism Designed Only for Thought, sounds a lot like M.O.D.O.K., the Machine Organism Designed Only for Killingnote , not to mention being sought by much of the cast for his introductory storyline.
- The last man to remember the Old War (when non-human intelligences first demanded to be considered "real people") is Dr Collodi. He later turns out to have built multiple living animatronics.
- The Caucasian side of Unity's head has blonde hair in a bunch, the African-American side has black hair in an afro puff, as a shout out to DC Comics' Harley Quinn◊ and Marvel Comics' Deadly Nightshade◊
- Tip makes a reference to the "Paul is dead" conspiracy theory (he learns it from a secret document he found in the basement). A barely-visible sign in the same strip says "Beware of the Leopard".
- When the sentient silverfish ask what they could eat, Tip asks them to "just eat things no one cares about, like the Warren Commission files" (read here).
- Nick's wrongswears have included "Melon farmer", "Forget you" and "This is what happens when you find a stranger in the Alps".
- Marcie describing playing a video game with Chris, in which he tried to stop her destroying the ScreeWee fleet.
- Shelby Silvers, the bald, bearded representative of Annex One Maintenance, could be a reference to Shel Silverstein.
- When Sweetheart uses the drone to pose as a mad scientist her cover identity is Dr Nan Darling.
- Tip's name is also a reference to James Tiptree Jr., which in turn is why his gun is called Alice.
- Skin Horse's EU sister agency is called Counterpane, a reference to the poem "The Land of Counterpane" from A Child's Garden of Verse by Robert Louis Stevenson.
- In "If I Ran The Zoo", Tip passes various animals at the transgenic convention discussing how they can't trust Skin Horse. At one point this includes a doe and her fawn. The fawn says "What is it, mother?" and the doe replies "Danger. MAN is in the hotel."
- In "My House is Me", Tip's "Princess Training" has Mary the animatronic doll as a Drill Sergeant Nasty, which at one point becomes a riff on An Officer and a Gentleman.
- Jonah and Nera's big conspiracy chart, as well as a ton of Continuity Nods and genuine conspiracy stuff, features "the 19th Story" and "The Men with the Attache Cases", "Chu Industries", "Gippart International", "Tape 0ZK001 0ZK016" and "The Gray Man" and probably more.
- The three MacGuffin Man-Portable Fusion Reactors are named Luigi, Beni, and Victor, after the three Italian robbers in the L. Frank Baum story "The Box of Robbers".
- G.O.D.O.T.'s decription of the Little House is a paraphrase of the opening lines of The World is Round by Gertrude Stein.
- A Life in the Woods parodies Annihilation with a little bit of John Carpenter's The Thing (1982) thrown in for good measure.
- When Tip asks Venus about the Old War, she replies "Ah, that is another story and shall be told another time."
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