Aerith and Bob: There are people named Surma, Antimony, Gamma and Zeta and Sir Eglamore as well as Jack, Janet, James and Andrew Smith, whose magic power is to make things orderly.
All Myths Are True: According to Jones, Coyote did place the stars in the sky, and so did every other mythological being attributed this task, but she also claims the stars have also always been there since long before Coyote and co. existed.
City of Adventure: Gunnerkrigg Court — a school resembling an industrial complex the size of a city (with its own park!), just next door to a creepy forest.
Dark World: A dark city, the evil twin of Birmingham.
Eldritch Location: The Forest and the Court don't exactly fit in normal reality. For one, the Court is an enormous city, with multiple parks, lakes, and power stations, but it's almost completely abandoned, and seemingly stretches on forever.
Extranormal Institute: The Court. Virtually everyone inside it is some manner of bizarre, or related to people who are. There seem to be a few baseline Muggles but they typically have oddities in their jobs, like Eglamore being a Dragon Hunter.
The bridge to Gillitie Forest. It's wide enough to not be immediately dangerous unless people walking on it do something unusually stupid, and it lacks railing, since any shadow cast on it would allow the Glass-Eyed Men to cross it at night.
Wizarding School: The court is a subversion. Even though magic occurs on school grounds, the court considers any and all phenomena as scientific.
The World Tree: A Cherry Tree (from Gillitie Woods) in the artificial habitat room; it is there Annie starts to open up to Kat. In "Divine" there is a callback to the tree as a place where Annie can put aside her "mask."
Narrative / Themes
Aborted Arc: The paintings from Chapter 2: Schoolyard Myths, as seen in page 7 were supposed to be part of a sub plot, but Tom has since dropped the concept.
Absurdly Sharp Blade: The tooth Coyote gave to Annie in Chapter 26: The Old Dog's Tricks. On Kat's official sharpness classification, said blade is "Really damn sharp", to the point of cutting a shadow from the floor. But it doesn't cut Shadow himself, fortunately for him.
Coyote: The keenest blade you will ever find! Be careful with it, because it could cut the very earth!
One day I saw a pigeon fall from a tree, its body twisted and broken from an attack somewhere above. It writhed on the floor in silence and eventually died. It had no expression, just as I have no expression. I have never relayed this story to anyone.
Breaking the Fellowship: Surma, Anthony, Eglamore, Anja, Donald and (presumably) Brinnie were one inseparable company as students and perhaps for some time later, but before the story started, Surma left the Court and broke all contact with the rest except Anthony, and it's unknown yet when and where Brinnie has gone.
Breather Episode: After the Wham Episode that was Chapter 39 with Coyote's "great secret", Ysengrin going batshit and the reveal that Coyote's been fucking around with his memories, Mort Fun Time was a welcome respite.
The etheric scar which Annie received from Jeanne's sword in Chapter 8 has been repeatedly alluded to throughout the story, as it remains on her face, clearly visible to all etherically sensitive individuals. Its true significance still remains a mystery.
Eglamore handed Annie a beacon just in case she was ever in trouble while visiting the Wood. After being forgotten about for chapters, she finally gets to use it.
The power buttons on top of the Seraph robots' heads. Loaded under everyone's noses all the way back on page 9 finally gets fired on page 1141.
The incredibly metaphor dense nature of some of the symbols makes a lot of future plot points hinted at way in advance of their actual usage. For instance, the rocket shown at the end of the first year foreshadowed an actual rocket launch 700 pages, 2 in story years, and several real life years later.
Chiaroscuro: In the etherium, everything seems to glow in the dark, and highlights and shadows alike are more pronounced than in the ordinary world.
Comically Missing the Point: Jones basically compliments Annie in this page by responding to a description of Shadow's friendliness and open-mindedness with "He sounds a little like you, Annie.", but Annie takes it literally.
Cringe Comedy: The strips of Jack trying to hit on Annie after he was freed from spider control were painfully awkward for the both of them and the audience.
Crossover Cosmology: Reynardine and Ysengrin are based off Reynaerde/Renard the fox and Ysengrimus the wolf, respectively, from Medieval European folklore. Muut, Coyote, and the Glass-Eyed Men are from Native American myth. There's also several ghosts, fairies, and, for good measure, a flashback montage featuring every Psychopomp, ever. Chang'e, Brynhildr, and the Minotaur (of Chinese, Norse, and Greek mythology, respectively) have also made appearances.
Antimony: Coyote, can you tell me, what is Gunnerkrigg Court? Coyote: Why... It is man's endeavor to become God! How is that for an enigmatic answer? Ysengrin: Very enigmatic. It barely answers anything at all. Antimony: In fact, it raises more questions than before.
Curiosity Killed the Cast: Not the lethal kind, but there were rather close calls. Curiosity also starts several plots, and often proves helpful when combined with compassion.
In one of Dr Disaster's simulations Smitty finds the MacGuffin almost immediately because of his ability to create order.
Day In The Life: Played with in ch. 40, which, for several pages, is a series of past events in Jones' life, from the day before the first page's events to billions of years previous. Little's been revealed so far except that the next medium has been chosen, based on Jones' recommendation, the previously-hinted-at relationship between Jones and Eglamore has a lot of layers to it, and that Jones doesn't age, and part of her taking others' names is to keep this a secret. She also doesn't consider herself to be alive, and doesn't know what she is.
"Spacemonauts! The evil Enigmarons are threatening the Earth from their moon base on the moon!"
The creepy space aliens from outer space.
Do Androids Dream?: The Court robots seem to have personalities and their own society out of sight of the humans, and they are explicitly trying to figure out their "purpose" beyond merely being custodians of the Court. One of the biggest questions they seek an answer to is why their creator, Diego, would engineer the death of someone he loved. They also think of Kat as an angel.
Bob: Hmm, there's a lesson in all this... (...) Never let sixty angry kids use a herd of laser cows to take over your house.
Fling A Light Into The Future: The original Magitec robots didn't have the means to reproduce, so they designed the modern court robots as their successors.
Flipping the Bird: Since he doesn't have fingers, Reynardine does the "up yours" equivalent to Annie for being put in timeout.
The Force: The Ether, which, like the Trope Namer, infuses all living things, can be directly harnessed only by a few humans, and bestows upon its users the abilities of telekinesis, clairvoyance, teleportation, flight, and superhuman speed and jumping abilities, and can even be used to create Magitek like 'etheric computers', which can project Deflector Shields or bind people/things if their users will it.
The Glass-Eyed Men seem to be made of pure shadow, but Kat deduces that they're actually just very thin layer of matter that may as well be a layer of light. Or, you know, dark.
Harmony Versus Discipline: In just about every sense, from magic, nature, and world view, the Court and Gillitie woods are opposed. The Court favors rational methods, control, and gray expansive industrialization. The Wood represents nature, unbound and at times terrifying.
Hug and Comment: Chapter 32 ends with Annie and Kat hugging, and then Kat saying "Annie ... I love you and everything, so ... it is with love that I must inform you that you really gotta take a shower."
Paz: The Court isn't a big monster that does as it pleases. Es a collection of people, working to do what they think is right. And, over time, other people see what is wrong, what mistakes were made, and work hard to fix them.
Kat gets another one after her opinion about the Court changes in Chapter 29.
And once again, Annie and Kat have noticeably different hair after the summer holiday between chapters 31 and 32, Annie having grown hers longer than it ever was and begun to tie it back, and Kat having cut hers shorter than it ever was, accentuating the growing rift between them.
Kat completely unabashedly tossing off this line is just one of the many ways she's so very lovable.
"It may be empty but it's full of potential!"
Annie's attempts at humor are a bit more...forced.
Info Drop: This was standard practice in the early run. At the end of each chapter was a bonus page, giving details of the school and surrounding areas.
Insomnia Episode: Zimmy doesn't sleep. When infected with the spiders around Zimmy's mind, Jack Hyland also becomes sleepless for a short while, and gets more and more mentally unstable until Zimmy finally removes them.
Ironic Echo: Eglamore responds to the students' complaints about camping in the cold with "Good question. Night!" At the chapter's end, the sleeping arrangements have reversed, and Annie tells Eggers: "You know where the tents are. Night!"
Is That What She Never Did Tell You: Annie collected a heavy basket of this looking for answers in all the wrong places. Now this began to hit her, mostly in the face. When she finally talked with her mother's best friend directly, she made some... little discoveries. Like why Surma left the Court to never return, or related to Annie the tales of Coyote but didn't mention knowing him or say anything about other notorious inhabitants of Gillitie Wood she knew at least as well.
Laser-Guided Amnesia: Coyote removes the memory of Ysengrin's insane attack on Antimony (and possibly more than that) from his mind, against his will. This apparently isn't the first time this has happened, by far.
Letter Motif: Gunnerkrigg, Gillitie, Good Hope: the letter G seems to be important. One wonders what this implies about Miss Gamma Czarnecki.
A Light in the Distance: Annie, lost and alone in the Annan gorge, sees a light on the opposite shore. It's Jeanne. Things don't go well.
Limited Wardrobe: Averted. The characters wear all kinds of clothes, appropriately to the situation. And the two female protagonists even change their hairstyle regularly.
Literal Metaphor: Both Renard and Coyote repeatedly told Annie almost word for word "You have a fire in you, fire that belonged to your mother". This turned out to be not a runaway compliment, but a fairly straightforward, concise and accurate statement.
Magic A Is Magic A: It's implied that all magic follows specific rules. So far, the best covered is Rey's Demonic Possession — e.g. he's able to occupy a toy simply because it has eyes.
Reynardine is also bound in the wolf toy and forced to obey Antimony because he chose to inhabit an item she possessed ownership of, which is why he hasn't just jumped to something else.
Also, when Coyote gives away a power, it gains a side effect it didn't have when Coyote had it, like Ysengrin's artificial tree-body and his atrophied real body, and the fact that if Renard takes over a body, it dies when he leaves and the original owner is extinguished when he enters.
There's also the fact that any power Coyote gives, he can't use until he takes it back.
Magic Versus Science: Mostly because their philosophical disagreement between their practitioners. Ironically, mixing the methodologies seems to bring the most impressive results and according to a history lesson by Jones may have been the Court's purpose in the first place.
Coyote's "interesting thought experiment," as Jones calls it: he says he put the stars in the sky and that's true (ditto for all the other powerful beings who claim the same). Jones knows the stars were in the sky before anything existed to put them there (or imagine the things that will put them there) and that's true too.
Mood Whiplash: Typically occurs for both the characters (i.e. as a narrative trope) and the readers at the same time. Best example so far is probably the scene where Ysengrin goes berserk and nearly kills Annie, and Coyote forcibly removes his memory of the incident. Next page, Mort Fun Time!
Mundane Utility: The blinker stones' amplifying powers have a wide variety of uses, including signal rocket and instant campfire; Annie has used hers as a torch and a psychic walkie-talkie, among other things. It also comes in handy for temporarily blinding Ysengrin when he's chasing her and Eglamore out of the forest.
Non Answer: If you ask any of the court's residents how the court was built, they will just say that the founders made it. If you ask anyone else who might know, all they will say is that "It grew from the Seed Bismuth."
Kat's father is very happy when he realizes that the coded message Antimony's father sent makes sense once you include him saying Antimony's name at the start, until he realizes the implications this has for an already upset Annie.
Ysengrin, after Antimony flicks Coyote's nose as her way of saying she won't tell him stories.
Our Demons Are Different: Reynardine and Zimmy were called demons at some point. No guarantee in the first case it was not a popular simplification, and the second was confirmed to be only an invective.
Our Dragons Are Different: Rogat Orjaks ("horned giant" in Slovenian) are explicitly stated to be dragon-kin, but not the same as "usual" dragons. One is quoted making a distinctly Take That remark on the subject of "those [common dragons]".
Our Fairies Are Different: "Regional Fairies" are so-called because they have spots on their shoulders showing which "region" they're from. They learn little kinds of magic (like rusting metal) and are said to come of age when they make their own clothes. "Red" and "Blue" are the only ones introduced in the main story. Others appeared only after becoming humans, as students in the Foley house.
Our Ghosts Are Different: Mort, the Ghost with the Sword, the dead boy in the hospital, a blind man's ghost mentioned by Kat in her letters over the summer break, and the dead couple haunting the musical instruments are all different from each other. This will probably all be explained eventually. Maybe.
Shadow Archetype: The recurring theme of duality in the narrative makes this fairly common in both characters and other elements of the world, though it's sometimes difficult to tell who or what the 'shadow' is.
Coyote: If you tell anyone in the forest about the tooth, even Ysengrin, this bind will snip off your hand.
Trickster Mentor: Seems to be the Court's established modus operandi, at least to a degree: it's the playground for the individual initiative, even if it's occasionally acting "against" the rules or teachers. The unwritten rules seem to include "It's your project, tell me when you finish it" and "Not Cheating Unless You Get Caught". They also teach reasonable level of cooperation.
They have security measures clearly designed to provide a reasonable level of challenge for students inevitably bypassing them, such as obvious and regularly hacked motion detectors, or security robots that we saw circumvented with tricks, hacking and plain outrunning — compare this to their outrageously advanced and subtle technologies like the tracking system.
Unfortunate Implications: invoked The first time Annie's father contacts her in years and it turns out to be a coded message. A coded message that doesn't make sense unless you include her father calling her name at the start of that message.
Annie: So... my name was just part of the message? He wasn't really calling me at all?
The Unreveal: Ysengrin told Annie what Jones was. Or tried to. We, however, were not privy to that conversation.
When Jones herself gets around to giving Antimony the longer version of that story, it turns out to be much, much longer. Jones' conscious recollection begins with the formation of planet Earth itself; even remembering all that, Jones doesn't know what she is, and says she isn't technically immortal because she doesn't even consider herself alive.
Weaksauce Weakness: The Court's Seraph model robots are capable of flight, very capable in combat, immune to electro-disrupters, and can be turned off just by pressing a big red button on the top of their heads.
Artificial Limbs: In a bizarre reversal, Robot was given a prosthetic arm made of wood.
Big Guy, Little Guy/Fat and Skinny: The two ghosts unleashed by John and Margo. The male is short and fat, the female is tall and thin; unfortunately they don't get much characterization other than they're terrifying and in love and just want someone to finish their song.
Blue and Orange Morality: Annie and Kat ran into this trying to reconcile two ex-fairies. According to the fairies, mutual understanding and respect are not the most important things for choosing your friends, it's cool hair. Later it turns out that once reconciled, these two taunt each other and fight all the time. Other Foley kids merely see it as a sign of strong attachment.
Generation Xerox: Subverted when appears. This generation of protagonists are descended from parents who were also adventure buddies back in the day — but the two generations are different in just as many ways as they are alike.
Directly defied by Mr. Donlan to Antimony eventually. Antimony for one is glad to be treated as her own person instead of her parent's child, especially soon after this got more unsettling.
Gentle Giant: Quite a few, such as Lindsey the giant crab. In fact, it's almost a reliable guarantee that the bigger and more intimidating someone (or something) is, the nicer they're going to turn out to be. Eventually lampshaded.
Humans Through Alien Eyes: On Andrew's first trip into the forest, he meets a Chickcharney who has lost a treasure he received long ago. A "shining sphere of unmelting ice! Trapped inside were brilliant colours from the rarest flowers". Andrew immediately produces a marble. "Did it look like this?"
Also, a slight shift when Annie is using the Blinker Stone. (Everything is generally more detailed and her hair connects panel to panel.)
Art Evolution: Tom is consistently evolving his art. It's most noticeable in Annie's case: Compare her design on page 18 with her design on page 435 (which, incidentally, is a Flash Back to the same scene from page 18). Now compare with page 1148.
It's even lampshaded in this strip, which refers back to an earlier incident in which Annie tricked a group of robots by disguising herself as a robot. The robots have drawn a Wanted poster of the unknown "robot", complete with football-shaped head. (One possible explanation is that the changes in art style reflect actual changes as Annie matures physically.)
Deliberate Values Dissonance: Used to comedic effect between the friendships of humans and the friendships of fairies. Also pointed out to be a dominant cause for the strained relationship of the court and the woods.
Early Installment Weirdness: Mechanically unskilled Antimony building a robot (since Retconned), Basil the Minotaur living in the Court's basement, Zimmy willingly partaking to a large gathering of people with no visible signs of discomfort, and many other instances conflict with the setting and the characters of later chapters.
Fisheye Lens: When things aren't quite normal and/or there's an actual camera involved, and to emphasize Annie's Heroic BSOD.
Most of the stuff is related to the events and reveals of Chapter 31: Fire Spike. Chapter 3: Reynardine introduces us to Renard himself. At one point, he recognizes Annie as Surma's daughter, and is sad when he concludes that Surma is dead. At some other point, in a flashback in Chapter 18: S1, the one who is sad is Anja, after reading Annie's transfer letter. In Chapter 20: Coyote Stories, Coyote tells Annie of the origins of both the Court and Gillitie Forest. At some point, he says "There were some humans and creatures living on both sides. Many of the current inhabitants are descended from those humans". It turns out that Annie is a descendant from a fire elemental. From Chapter 21: Blinking, page 28: "The day Surma died, none of us came for her." and "I had to do it myself." From Chapter 23: Terror Castle of the Jupiter Moon Martians, Renard does a comment towards Annie: "You have a fire in you, child, a fire that belonged to your mother!". This turns out to be a Literal Metaphor.
In the bonus page of Chapter 11: Dobranoc, Gamma, Zimmy wants to chase spiders. Cue Chapters 27 and 28: Spring Heeled, where it's revealed why they need to be chased down.
In Chapter 39: "The Great Secret" when Coyote explains that mythical beings such as himself are created from the minds of humanity, Annie objects that this doesn't explain Jones. In Chapter 40: The Stone, we learn that Jones predates humanity by a considerable amount of time. (Coyote, of course, says that it does explain Jones, but doesn't say why.)
Girl on Girl Is Hot: Invoked by Reynardine when Kat and Antinomy are having a heartwarming moment. Plot point, too, because it's the reason Antimony orders him not to speak until she commands it.
Chapter 30: The Coward Heart goes from being reasonably upbeat, to horrifying revelations about a character's death, then the same character trying to kill the protagonists... and finally then ends with two characters admitting their love for each other.
Chapter 31: Fire Spike - It begins with undefined unease, explodes into anger, and ends in tears.
Chapter 39: The Great Secret - From silly (fun times with Coyote!) to Wham Line ( the aether is human imagination!) to scary ( berserk Ysengrin!) to Wham Episode ( Coyote eats Ysengrin's memories to make him loyal!) and finishing off with MORT FUN TIME.
Never Trust A Title: Chapter 34: Faraway Morning (And Three Short Tales), where some characters tell three short tales. Sounds like a short chapter, right? It's the longest chapter to date thanks to all of the Character Development and plot revelations going on between each of the tales.
Reclusive Artist: Tom Siddell is known for being very private about his personal life. All we know for sure about him is that he lives in Birmingham, used to have a job as a graphic artist at an undisclosed video game company, and is pretty good friends with Magnolia Porter.
Tom's comments below each comic sometimes are variations of Epileptic Trees, the line "Oh. It's that guy." or "[Obvious event in-comic]! ([Obvious event in-comic])". Or explaining who is/isn't Mr. Eglamore. When Trees Attack, "Eglamore looks pretty different. (This was a joke, that is not Mr. Eglamore)". When the Minotaur returns, "It's this guy! (It's Basil, not Eglamore)".
At one point in a flashback between Eglamore and Jones, the page caption was, "Reassuring?". Everyone in the comments demanded to know who the strange man on this page was.
If Jones keeps beeping like that people are going to get the wrong idea.
Schedule Slip: Not the webcomic itself — Tom has maintained a 30-page Strip Buffer since day one — but both published volumes didn't hit shelves until months after they were scheduled to come out. The delay of Orientation was bad enough that Tom thought Archaia was defaulting on the publishing contract.
Series Hiatus: Several times, each one lasting, at least, two weeks, and coinciding with the end of each book.
The first was after the end of Chapter 14: The Fangs of Summertime. In the timespan between this chapter and Chapter 15: Red Returns, bonus material and guest comics filled that void.
The second hiatus occured after Chapter 22: Ties, and this time it was the omakeCity Face.
The third hiatus happened after Chapter 31: Fire Spike, and, like the second time, featured City Face 2.
The fourth hiatus happened after Chapter 41: Changes, and featured in-universe cartoons about City Face, ostensibly drawn by some of the comic's main characters.
Shown Their Work: Attention to fine details in itself became yet another layer of fun. If something looks dubious, usually this get fixed by more research on the viewer's part. Mongolian draw and archery bracers? Baby pigeons◊? Canine skulls? Moon pools? A girl musses her hair up after removing the hair tie? Check-check-check...
A very subtle one. One of the strips is just a random collection of real photos. One of the pictures is of a mineral called Stibnite (it's easily identifiable by it's bladed crystal habit). Not only is that briefly mentioned as Surma's maiden name at one point, there's also the fact that the mineral contains an element that isn't found in many minerals; Antimony.
The Laser Cows all have a serial number that starts with LC. Elsie is a popular cow's name, thanks to being the name of the mascot of the Borden Dairy Company since the 1930s.
This◊, directed at someone who complained that the flashbacks weren't made obvious enough. There were a few "helpful" notes for those who get disoriented by the Art Evolution, take jokes too literally or both at once.
Tom's◊ reaction to a weekend of speculation that Jones is a robot, months after Reynardine told Annie that she isn't.
Viewers Are Geniuses: It helps a lot that the forum community is comprised of readers from all over the world (some of the most frequent posters are from places like Russia, France, Spain, and Alaska) and so most mythology symbols, folk songs, and bilingual bonuses can frequently be first noticed/explained by a native of the region in question.
There was one instance when the fandom (using a bare minimum of information) figured out that Brinnie's "Old Man" is Odin from Norse Mythology, and shortly after, that Brinnie herself is Brynhild the valkyrie. The full extent of the information they had? Brinnie is Scandinavian, and she uses triangles in her magic.
Less than a day of this page going up and people wondering whether the girl was Chinese, Japanese, or Korean, a bunch of posters on the Gunnerkrigg forum immediately identified her from Chinese mythology.