Genius Bonus: The screen names of the all the trolls and kids (using John's former ghostyTrickster handle), when shortened to initialisms, use only the letters G, A, T, and C, which are the letters/abbreviations used in sequencing DNA.
In addition, John changed his initials from GT (a legitimate dna sequence) to EB (which has no corresponding sequence) in an attempt to lose the trolls pestering him (especially Karkat). In short, Karkat's trolling created a mutation in the code: he gave their universe cancer in every way imaginable.
uranianUmbra and undyingUmbrage (Calliope and Caliborn) may seem like exceptions, until you realize that U is the RNA equivalent of T.
Genre-Busting: Equal parts comic, novel, game, animation, and more.
God Never Said That: Begin Intermission 2. Cue hordes of MSPA forumers getting worked up over the fact that Lord English has a pegleg just like Squiddles antagonist Skipper Plumbthroat! There's only one problem: Plumbthroat doesn't have a pegleg. Take another look.
Also seen here, when John is ironing his pants. Though they appear to only be green blobs, they are presumably green slime ghosts.
Gone Horribly Wrong: The last few sessions of the SBURB haven't been going well at all: Beforus' trolls didn't finish and had to scratch their game; Alternia's trolls didn't become the gods of the new universe and gave it cancer; Earth's Beta kids had to scratch their game; Earth's B2 kids game is "void" and won't produce a new universe, and because Caliborn killed Calliope's dreamself (not only making a solo session but dooming him to being an "emotionally stunted little tool" forever) the Cherub's game is "dead".
Gone Horribly Right: Beforus' trolls were too weak and distracted with teen drama to finish the game and had to scratch their session so Doc Scratch ensured they the new version would be aggressive enough to finish; Alternia's trolls bulldozed their way through the game and ignored its finer points.
Guide Dang It: invoked All players in a session must prototype their respective Kernelsprites at least once before entering the Medium; failure to do so renders the game Unwinnable. The game comes with no documentation, and there is no guarantee the players will figure out that "prototyping" is even a thing they can do, let alone a thing they must do within a certain timeframe. The Kids only realized this after their session was nearly complete. Fortunately, not prototyping is more difficult than prototyping, due to predestination.
It's worse than that. After realizing the sprite will help you on your quest, the logical thing would be to throw the most powerful thing/person you know in there, right? Wrong. All the enemies get stronger with your prototyping and if you used something powerful (like Becquerel or Feferi's lusus), you are screwed. Worst of all, there's absolutely no way to know any of this until it's too late, so the logical sequence of events is for kids to prototype really powerful things early on (before they realize it's empowering their enemies), then completely halt prototyping altogether for people who join later (after they realize it's empowering their enemies, and without realizing that if anyone skips a pre-entry prototyping, the game is immediately Unwinnable.)
In-setting, the Trolls were lucky enough to have access to the guide written by Rose via Timey-Wimey Ball shenanigans.
Hailfire Peaks: Pretty much every land is some combination of two stock video game settings, expressed as "Land of X and Y." All lands have ruins as well.
Hair-Trigger Explosive: Unsuccessfully invoked in the Midnight Crew intermission by Clubs Deuce, who once wears a lump of C4 on his head before charging with his cane (apparently made from bovine attribute skin) in hand:
Stitch says drop the livestock knob and settle the hell down. He says you do realize C4 is a stable explosive and won't detonate with gunfire, right? You say oh.
Hammerspace: The Sylladex can can hold some enormous things without weighing down the owner. However, there's a limit to the number of things it can hold, and managing it can be frustrating.
Hanlon's Razor: Played for laughs during the Intermission when Fin is aghast at what a diabolical mastermind Clubs Deuce is, when in reality the little guy is just wandering around admiring clocks with no clear plan of action.
Harder Than Hard: Doomed sessions are eventually described like this, with dead sessions described as playing on extreme difficulty.
Dead sessions aren't just Harder Than Hard. They're a complete departure from the standard rules of the game.
Heart Is an Awesome Power: Most of the aspects are rather straightforward, but a handful seem sucky, initially at least. For instance, the Heart aspect actually translates to souls. The two Heroes shown with this aspect (Dirk and Nepeta) respectively can destroy and steal souls.
Hope is also apparently a very potent aspect, though its literal meaning is still ambiguous.
Hello, Insert Name Here: The initial introductions of some of the main characters prompts the player for their name. This continues to its logical conclusion, naming a planet.
As if that wasn't enough to establish it as Hell Is That Noise to the characters, then came "[S] Equius: Seek the highb100d". After you enter the vent as Nepeta, it's dark, you have no idea where Gamzee is, and all the music stops save for... this. And you can hear the honking.
The honking also turns out to be the noise Lord English made to announce his birth into the universe. And his sole purpose for existing is to ensure a universe's destruction.
Far earlier, Tavros mind-controlled Becquerel and made him teleport a speeding bullet from "towards Jade" to "towards the adult intruder on her lawn". Unfortunately Troll culture is unfamiliar with the concept of children being raised by their parents, and the "intruder" was actually her Grandpa.
In a more tangled example, Her Imperious Condescension also mind-controls a sprite-fusion of Jade and Becquerel.
Homoerotic Dream: When discussing Dave's dreams, Rose insists that they are simply bursting with phallic imagery.
Hope Spot: The alpha kids were disorganised and pitted against each other after Dirk and Jake's breakup, but reconciled after the end of the Trickster Mode. Then, they are killed by Prospit and Derse's moons exploding and ascend to god tier. Then, they are confronted by an overpowered Jack on Prospit and the Condesce on Derse, and seem almost powerless to stop them. Then, Jade comes to the aid of Jake and Jane, and things seem to be in their favour. Then, the Condesce uses her double mind powers to make Jade go grimdark, and then controls her into retrieving Jane's tiaratop, also putting her under the Condesce's control.
Humanity Is Infectious: Traits that the Troll culture regards as sickening - and exhibited by the protagonists - start to seep into their behavior the longer they interact with the humans. In Vriska's case, she gets Perverse Sexual Lust for one of the characters in one of John's favorite movies.
Humanoid Aliens: The exiles and the agents are two-armed, two-legged, and have endoskeletons and exoskeletons. The Trolls look mostly human, save for their grey skin and horns.
The Trolls also have no nose when Hussie draws them in more detail. The best place to see it is probably John:Enter Village - John has a nose, while Vriska does not.
I Know Your True Name: Inverted: Caliborn can be put to sleep by waking up Calliope, and vice versa. Unfortunately, both times the B2 kids tried that they failed, since her dreamself had been killed already.
Imagine Spot: A few characters indulge in these from time to time.
Imagine Spotting: When Aranea begins her story about "two legendary rings," the next page has John with an imagination bubble above his head that shows the four-orbed queen's rings worn by Bec Noir and the Peregrine Mendicant. Aranea shoots down that train of thought immediately.
"No, not those rings!"
Immediate Self-Contradiction: In Kanaya's introduction. "You are one of the few of your kind with JADE GREEN BLOOD. As such you are one of the few who could be selected and raised by a VIRGIN MOTHER GRUB, an event so rare as to elude documented precedent."
Inexplicably Identical Individuals: Dad Egbert and Dad Crocker may be an example, since they seem to not be clones of each other but still appear identical. On the other hand, their appearance is not entirely literal, so it's not certain that they are in fact identical.
Info Dump: The recaps ended up confirming and clarifying a lot of info.
Infinity–1 Sword: Caledfwlch, the sword that Dave's quest centers around. By the time he gets it, he already has an upgraded version from the future, and the present day Caledfwlch is repaired and upgraded into the Royal Deringer...until combining the Deringer with a magic cueball produces Caledfwlch all over again (showing that while it is not as strong as the Deringer, it is still the most useful sword for opposing Lord English).
Insistent Terminology: The Green Sun is always written in green with flickering letters (using an image file).
Similarly, The Tumor is always written in black, at least until its appearance is known and then it's TheTumor ("Black-and-whitened for giant yin-yang bomb.")
On the other note, all supernatural mindfuck of Homestuck is not magic. Even when it's done with wands, called a spell, and definitely has nothing to do with laws of physics, it's still not magic. Magic is fake.
Insignificant Little Blue Planet: Trolls initially keep verbally dismissing humans as insignificant creatures from a small planet. Then it turns out humans are both the source of their problem and its solution, and are actually a lot more smart and competent overall. And anything but insignificant, seeing how they created the source of all energy in the Universe(?).
CG: MORE OF THIS NARCISSISM. CG: YOU ALWAYS THINK EVERYTHING REVOLVES AROUND YOU. CG: WE HAVE NOTHING TO DO WITH YOUR DUMB LITTLE WINDY PLANET OR YOUR PETTY LITTLE QUESTS.
As a subversion of the usual trope, the insignificant planet being discussed in this specific bit of dialogue is not Earth, but John's game planet, LOWAS (the Land of Wind and Shade). It is mainly blue (which is sort of John's Arc Color), though.
Interdimensional Travel Device: Fenestrated walls. Normally they're used to observe faraway places, but smashing through the wall allows one to travel to the location. Andrew Hussie breaks through one of these walls to get from his house in Real Life to Doc Scratch's house in the trolls' universe. Later, Jade and John use another of these walls to escape a universe that's being written out of existence.
Interface Screw: Disk 2 of Homestuck is damaged because Terezi tried to use it with a record player. The result is... odd.
The results of Caliborn taking a crowbar to a computer tower is possibly even odder.
Caliborn manages to hijack the narative prompt, and sabatoge the Act 6 cartridge, causing it to become glitchy like when Disc 2 was scratched.
Interface Spoiler: Sort of. Meenah's name is initially revealed not by anyone saying it but as a property of the "dialoglog", where her spoken lines are displayed after her name. John and Roxy aren't made aware of her name at the time, but the reader is.
Inventory Management Puzzle: Part of the humor of early acts was the increasingly ridiculous Moduses that characters have to deal with. This recurs briefly at the start of Act 5 and Act 6 before fading again.
Item Crafting: Just put two punched cards in the TOTEM LATHE at the same time. John's since thought of punching a card twice, each time with a different code. As an amateur programmer, he's become about as aware of the possibilities, quirks and limitations of the system as the readers in the forum. It turns out that if combining items via stacking cards combines a pair of items one way, double-punching their codes will combine them in an opposite way.