- It's Hammertime for Tarvek!
- The Heterodyne Castle has the grave of a guy called "Iscariot Heterodyne" with the line claiming him to be 'everyman's "friend"'. The quotes around friends are intentional, because the skulls of his "friends" are piled up right next to the grave, hinting him to be an notorious traitor like his namesake Judas Iscariot from the New Testament.
- This page sports an Steam Punk version of the hut of Baba Yaga, with mechanic chicken feet and the egg joke.
- The very first page contains The Winslow.
- The wiki has a whole list of the ones to other webcomics. In Mechanicsburg, there are signs advertising for "exotic Wapsi Square", an inn called Gunnerkrigg Court, Professor Milholland's "Something Positive" tonic, a certain Dominic Deegan ("Sees all, tells all") and "The Devil's Panties" lingerie, among others... (Which get featured in the next strip.)
- Moxana is a shout out to both Moxon's Master and The Turk.
- Castle Heterodyne is equipped with Happy Fun Balls.
- In this strip, where several soldiers are attacked by a toothed trunk on legs with the words "The Amazing Pratchett" written on it.
- Another Discworld shout out is in the commentary: "...kicking and screaming into the Century of the Fruitbat", hmm?
- "Don't drink the wine!"
- A fairly unsubtle reference to Gil rescuing Zola from "some overly dramatic maniac who lived in the Paris Opera House."
- A skeleton of a giant spiky beast inside Castle Heterodyne was apparently a pet named Towser.
- The Unstoppable Higgs' cap indicates he's a crewman on the ship Rozen Maiden.
- When posing as Agatha's parents, Punch and Judy went under the names Adam and Lilith Clay.
- Turning a dread castle into... a Dread Gazebo?
- Martian Tripods in the Baron's flashback and one of the Heterodynes' "My Vacation" pictures.
- One strip mentions an electric game with the little man and the gorilla. It also mentions a boat ride with singing dolls. What a small world it is.
- One scene shows a sign for both an X-ray and a Purple Ray.
- Crazy A.I. with SHODAN-like Dramatic Stutter.
- "You don't expect a knife to sing opera, y'know?"
- When Zola first shows up claiming to be the new Heterodyne daughter, Agatha complains about her being a terrible, cheesy actor. Zola's very next line? "Yonder lies the castle of my father!", a quote from The Black Shield of Farnsworth, which is generally considered one of the worst-delivered lines ever as the original actor had a very strong Bronx accent. usually rendered as "Yonda lies da castle of my fadda" to emphasise that Curtis was Not Even Bothering with the Accent.
- In this strip, Phil Foglio is shown singing The Beatles' "Ob-la-di, ob-la-da" with modified lyrics talking about oubliettes. Then, when the Jäger comes up through the floor, he asks "Nov shmoz ka-pop?"
- This strip has Major Resetti of the First Subterranean Mecha Mole Brigade.
- One of Gil's paper doll outfits has a triforce symbol on the gauntlet.
- Buck Godot T-shirt
- Gil's valet shares a last name with the employer of the most famous gentleman's gentleman in fiction.
- And his first name with the high school that Phil Foglio attended.
- If one looks closely, it appears that Doctor McNinja has an office in the hospital at Mechanicsburg. Which... explains a lot.
- Benjamin Rat appears in that same panel — and "Dr. Rothfuss" obviously goes by Patrick. (The Wise Man's Fear was published three days after that comic.)
- A poster at the Science Fair here: "Planet Earth: A Scary Go Round we live on."
- Klaus can kill you with the power of his mind.
- Is that Teal'c?
- Sir Dan?
- The nefarious Prince Aaronev Wilhelm Sturmvoraus is visually based on Phil Foglio's fellow webcomic artist and Dragon Magazine alum Aaron Williams, and his servant Nod is Williams's signature character, Nodwick. Also, Aaronev's dogsbody Artacz, who looks like a younger version of Artax from Nodwick, only with a shorter moustache.
- very obscure one: "I'm a genius! Ha! Take that, Brillat-Savarin!" A
- When Zeetha and Agatha check out armors, some of them look kind of familiar...
- In the Heterodyne Crypt, there is a grave marked only "Zod".
- Theopholous is trying to track down his father's lost temple in India, which somehow involves finding the "eye of the snake eater."
- The fake Jagermeister girls at Mamma Gkika's bar sing a modified version of the Andrews Sisters' song "Too Fat Polka."
- Their earlier song is a resetting of "The Beer Barrel Polka" and their show slash song for the "real" Jaegers seems to dance around "You can leave your hat on".
- When trying to escape a burning airship, Tarvek and a Jäger almost quote the MythBusters:
Jorgi: "Dot dun sound like explosions..."Tarvek: "You're an expert?"Jorgi: "Sure, hyu bust op enough schtuff, hyu learns all kinds ov tings."
- Klaus can walk into Mordor if he wants. Or Mechanicsburg.
- A shop in Mechanicsburg sells Eldritch Meat. Today's special, Shoggoth.
- The Cinderella parody features music by the P.D.Q. Bach Engine, whose operator bears an uncanny resemblance to Peter Schickele.
- Gil's Runcible Gun, which shoots sporks, references the "runcible spoon" mentioned in "The Owl and the Pussycat".
- The introduction of Those Three Jagers has them hanging from a gallows for days, which is likely a shout out to the late Robert Asprin's Myth Adventures series (Phil Foglio illustrated the comic version.)
- When Krosp first promises to help Agatha, she asks if she needs to get it some boots.
- When Agatha first enters Gil's laboratory on Castle Wulfenbach, we see Dr. Bunsen Honeydew's gorilla detector. Fittingly, there is a note attatched to it that reads, "NEEDS WORK".
- The Wyrm of Limmerick is the engine that made the "Konigsberg Run in less than twelve kilometers".
- One of the "many horrors used against us" is the... Weighted Companion Cube.
- ALL HAIL THE WINSLOW!
- When Rivet shows Agatha her collection of tools, Agatha finds a sonic screwdriver.
- The beginning of Chapter 6 in Agatha H. And The Clockwork Princess to a certain infamous play ......
Lucrezia: You sir, should remove your pants.
Judy: Indeed, it's time. We have all laid aside modesty but you.
Stranger: I... wear no pants.
Lucrezia: (Terrified, aside to Judy.) No pants? No pants!