Blank It: Where do we start? The authors apparently have names for all characters, but they're rarely revealed to readers. Practically everything in the comic has been given a name by fans:
The selectively intangible people whose hamlet was centered around the shovelbeam — Unsettlers, or Adumbrates
The female purple-dressed Unsettler that Lemmo named — Misty. Some readers had trouble getting out of the habit after the comic finally revealed her name to be Marina.
Wendall the cookie — Chip the Biscuitd00d
The two baby foxes that were created when the original fox (Socks) was split in two — Parasox
The giant bees with axes instead of stingers — Buzzkills
The giant gold-coloured robotic salamander...thing — Robomander
First Puppet - derisive name for the female lead and her dependence on Dominus, The Chessmaster.
The Inappropriate Wall - derisive name for a freaking recurrent pile of bricks.
Collateral Damage Man - derisive name for blah blah blah blah blah. Celesto Morgan
First Caste through Fifth Caste, Churchspace, Deegandrug, Glasswood, Invisible King, Jocks, Mookinsertion, Progenitor, Red Shirt Soup Wench, etc. The hatedom is practically rewriting the entire strip. (This just in, they are...)
Snuggles/Eyebuddy/Squiggly/Snuggl'thu'lu/TED - nickname for the tentacle eye thing of the chaos dimension, based on his Alternate Character Interpretation as an innocent childlike being who just wants hugs.
The Aardvark - Supergreg, the frail and crippled white mage after turning into an overt Superman expy in a medieval setting. How was this received? "The Aardvark" was coined later out of fear that he might come if his name was spoken.
Patches - A fan nickname for Jacob's necromantic golem before he received the name Quilt. Got referenced in the comic as a Discontinuity Nod.
Tess - Female!Tedd. Used in out-of-continuity strips longago. This convention spread as more characters switched genders, then overloaded when the entire main cast did and was replaced...
A Fan: fTedd is a female version of Tedd, who is usually male.
Tess is Tedd's analog in a different reality, and is always (as far as we've seen so far) female.
After all, if Tess was TFed into a male form, she wouldn't suddenly become Tedd. She'd be mTess.
You start mixing and matching your nomenclatures and you'll make discussion on this board an even bigger clusterfudge than it already is.
This practice was pretty much abandoned when a discussion thread revealed that no two posters had the same nickname for mGrace
Susman, Manase - mSusan and mNanase. It hurts, yet they cannot stop.
Rocky, Indiana Gandalf - The unpetrified wizard in a trenchcoat.
Mamase - Nanase's mom.
Gluece - Grace in context of "Grace glues everything to everything" fan-meme.
The two French immortals are generally known as Denise and Bernard, based on the names often used as examples in French textbooks.
Scarlet - Lady Sylvia Lazarus, a Unaroyal warlord. So called because of her red hair and the fact that her name wasn't mentioned until book 2 text update 8.
Da Boyz: the collective name for the Jagers Maxim, Ognian, and Dimo
Agatha's miniature mechas are called "Dingbots." They build more dingbots, creating swarms, although later generations are less capable than the originals. Their jealous adoration of Agatha has led to the suggestion that a swarm of dingbots be called a "devotion."
"Mamma's Girlz" is becoming popular for the three nameless fake-Jager barmaids in Volume 8.
"Der Kestle" is also becoming popular as a nickname for Castle Heterodyne, though to be fair the Jägers do call it that.
The GAP - Chief, Thaco, Complains, Big Ears, and sometimes Fumbles. Stands for Goblin Adventuring Party.
Thac0 - Thaco. This indicates that the poster is in on the gaming joke inherent in his name.
A lot of nicknames have been thrown around as shorthand for the various Alternate Universe players in the Maze of Many arc. Mostly applied to Minmax in particular due to how well his name lends itself to such things. PsiMax, MinMask, MinceMax, and so on.
Red and Blue - The two Regional Fairies from Chapter 8. Named for their respective hair color.
The second pair of fairies are also referred to by their hair color, but none of the fans can agree what those colors are. (Green, Teal, or Lime? Purple or Fuchsia?)
Suicide Fairies - The Regional Fairies who undergo the test to become human. (While this is a misnomer, since they Cannot Self Terminate, it's a heck of a lot more memorable than any of the more-accurate alternatives, like "Euthanasia Fairies".) Later used on the cast page.
Adminbot, the Guardbots, Horsebot, and Barberbot - Various robots, named after their job or appearance. (Following the example set when Tom Siddell referred to two other robots as Boxbot and Doorbot.)
Birminghell, Bummingham, Evil Birmingham, Zimmingham, Zim City - Zimmy's Black Bug Room, which was modeled after her (and the author's) hometown of Birmingham.
Not-Jones - Brinnie, before the revelation of her name, back when the only information about her was the Word of Tom that she and Jones are not the same person.
Chuckles - Ysengrin
Frankenbot (later abbreviated to Frank) - The first-generation robot that Kat reactivated, due to his resemblance to Boris Karloff's portrayal of the character.
HERO: It's hard to discuss a nameless protagonist, so HERO's nameless protagonist was fanicked "Lost", after Valentine introduces him by explaining that "He's lost. I said he could come with me," and Vin deliberately misunderstands it as his name.
Horace Focker for Sagittarius-themed troll Equius (centaursTesticle).
BLUH BLUH HUGE BITCH for Vriska Serket (arachnidsGrip), because she, well, kind of is.
Hass "The Flame" Harley for Jade's Grandpa, in a gag carried over from Sweet Bro and Hella Jeff.
"Fatferi" for Feferi (cuttlefishCuller), referring to the Fanon idea that she is overweight.
Eridan Ampora (caligulasAquarium) is usually called the "Douche of Hope" in light of certain events.
Before that, we just called him a douche.
John's new hammer, which people were nicknaming minutes after it was revealed. "Vriskammer" and "Warhammer of Vriskyhoo" are the most common though.
Turns out it's actually called the "Pop-A-Matic Vrillyhoo Hammer," so they weren't too far off.
"Kanpire", "Kanaya-pire", or "Vampaya" for Kanaya Maryam (grimAuxiliatrix) after she is transformed into a vampire.
Post-God-Tier-resurrection, Aradia Megido (apocalypseArisen) became known as Alive-radia.
Before his name was revealed, Doc Scratch was simply known as "White Text Guy."
When the authorshowed up wearing a Hero of Space God-Tier outfit, the hatedom promptly dubbed him the Waste of Space. This was funny enough that the actual fandom picked it up as a slightly more affectionate joke.
When Jade Harley ascended to the God Tier, and gained a pair of dog ears in the process, many people hit upon the pun "Dog Tier".
It had been floating around for a while before that to describe Jadesprite.
Jack wearing the Black Queen's ring has long been nicknamed "Bec Noir," so naturally PM wearing the White Queen's ring was quickly dubbed "Bec Blanche."
Karkat's guardian is commonly known as "Crabdad," while Vriska's extremely abusive guardian is "Spidermom." The former was actually mentioned in-canon as a Fandom Nod.
There's also "Goatdad" for Gamzee's guardian and "Seahorsedad" for Eridan's.
The Auto-Responder is commonly referred to as Shades Prick.
Before their names were revealed, Meenah and Aranea were known as "Punk Condesce" and "Nerd Mindfang," respectively, after their A2 counterparts.
During Act 5, Doc Scratch pulls a Hostile Show Takeover combined with Interface Screw, changing the look of the website. Fans called this the Othermission or [o]ntermission, after the "[o]" that preceded each command during the section. (The symbol refers to Scratch's cueball head.)
After a fan misspelled 'God Tier' on Hussie's Formspring, 'Got Tiger' has become a popular euphemism, as in one who reaches God tier has 'Got [the] tiger'
IFPODWTF (Infinite Featureless Plane of Death With Two Features): where the Deaths are based. Due to the fact that there are actually two features now: the Head Death's desk and Adam's Hole.
Two in-universe examples that have naturally caught on with fans are Glare Beam (Viktor's ferocious, one-eyed glare) and The Crazy Dance (Freckle's unfortunate tendency to go a little Ax Crazy whenever he's packing iron)
Niho: Miho's bishi male Endgames avatar, used to an extent that some people have mistaken it for canon, and remained in wide use even after the real name was revealed.
Yuki's Red Hot Mom: Meimi Sonoda, for being one of the most attractive women in the comic despite her kid's ages making her at least forty.
Kimizilla: Kimiko, the sweet, meek and slightly emotionally unstable heroine. Actually used as an insult in the strip itself, after she snapped particularly badly at her boyfriend.
Angry Schoolgirl: Often used to describe Largo's angry student Junko Ibara before fans actually learned her name.
The Darkly Cute One: Miho. Coined by a sketch that was posted some time before she appeared in the comic proper, and even longer before she got a canonical name.
Shy Guy: Yutaka Kobayashi, once again because the comic took a while before producing his name.
Not fan-based but in-comic-used and widespread throughout fandom are Belkar Bitterleaf's nicknames "Sexy shoeless god of war", "teh Belkster" or "Death's lil helper".
... better not mention not the nicknames Lawful StupidKnight Templar Miko get from the fans who dislike her.
Before readers ever saw Miko's face, she was known as "the Blue Guy". Once she was shown to be a female, but before she named herself, "the Blue Girl" was briefly used — or rather, avoided, thanks to its unfortunate resemblance to the title of a certain adult anime.
Pennies - Penny, Sara, Michelle, Brandi, Katy-Ann, and briefly The Mole Cyndi.
Scooby Gang/Scoobies - Aggie, Lisa, Fred and Daphne, based on those last two names and Daphne's (author-shared) love for Buffy the Vampire Slayer. Alternately, the AAA, "Aggie Artists Alliance."
iPod girl - Lisa, especially before her real name was revealed.
Injustice Gang/IG - Karen, Meg, Cyndi, Charlotte and Samantha; the author acknowledged the influence of the Justice League one, and the name stuck.
PAvengers - The team-up of the Pennies with the AAA to take down the IG. Cyndi, in her private journal, later gave them the In-Series Nickname "Peacies," after the peace-sign belt buckles they adopted post-"Popsicle War." Although she meant it derisively, this in turn replaced PAvengers as the standard Fan Nickname.
The combo of Unity (a fast zombie powered by nanotech goo) and Dr. Virginia Lee, with Unity injected into Dr. Lee: UniLee (although Virginity has also been suggested).
Dexter - The resurrected Head Alien of It's Walky!. Resurrectees in the comic are mirrored left-to-right. This moved Head Alien's claw to the other side, so he became right-handed (Dexter, in Latin).
Was given a Shout Out in Dumbing Of Age, which has a cartoon called Dexter, The Head Alien.
Britjas, short for "British ninjas" - the London-based secret agency run by Dargon Chesterfield (later Penny Worthington) which pulled the strings behind SEMME in It's Walky!.
Also called 'JFO' (Jason's Father's Organization).
The suggestion to call them UKKE (as a pun on SEMME) was not well received.
Nor was the suggestion to call them PMS (Penny's Marauding Stormtroopers).
Black Hat Guy of xkcd fame. Randall himself has even referred to him as such though it's never actually appeared in the comic.
The ZombieNarrator of Hanna Is Not a Boy's Name has no official name given, and is addressed by a different name every time Hanna talks to him. Some fans pick their favourite name, some follow Hanna's lead, some call him Zombie, and many refer to him as {...}. Or '...'. Or Dottie, or Dots, or Ellipsis. A very few have picked up the Victorian stand-in of ______.
Once his pre-zombified self became a popular subject of fanfiction after the release of supplemental art depicting him, he acquired the nickname Not!Zombie.
Also Conbat, Conrad's bat form. Followed by Casbat and Finbat, Casmiro and Finas as bats, and of course Sassybat, Conrad'sVampire Mom.