The Batman Fist, Teppei's Messiah Fist, a title given to it by friends in a RP because of Teppei's habit of firing its grappling cables at enemies. Those that get impaled by the barbs are similarly described as Batman'd
Footballhead — A derisive nickname for Renamon, whose head (according to said detractors) is shaped like an American football.
J-Reaper — ADR-01, the D-Reaper's Spy Agent, who was mimicing the appearance of Jeri Kato before mutating to a more monstrous look.
In the Japanese fandom, Masaru has gained Digimon status as Masarudaimon, thanks both to his returning appearances in Hunters letting him beat the tar out of Mega Digimon like nobody's business and to his own name lending itself to the Digimon naming scheme.
Veggie - Vegeta. As a sort of canon derivative, Ginyu actually refers to him as "Vege-Chan" a few times to taunt him. 'Geta is also used at times.
Kushami - Blonde, gun-crazy Lunch. Coined as shorthand by Curtis Hoffmann in his early summaries of manga chapters. It's Japanese for "sneeze," because Lunch changes personalities and hair color whenever she sneezes. Has reached the point where parts of the fandom are convinced that it's actually her name.
Mrs. Briefs - For Bulma's mother, since her husband is named Dr. Briefs. However, it is never actually clarified whether "Briefs" is actually a family surname or a given name (especially considering nearly everyone in Dragon Ball has Only One Name). The nickname "Bunny" was also seen in some fanfiction.
Shizuo Musou - the Shizuo vs. Vorona warehouse fight in volume 6
Tsugaru and Psyche - Shizuo◊ and Izaya◊ as they appear on the series' OST and cover song albums. Often treated as separate characters. Even more often shipped with each other. A new "character", Delic◊, has also been recently created in this manner with the release of the second half of the Durarara OST.
Pedo Teacher - Professor Nasujima, for hitting on Anri and generally being all-around creepy.
Jesus Beam - One of Toki's attacks, since he looks and acts a lot like Jesus Christ.
Sunagumo ("Sand Spider") - The Nameless Shura who defeats Falco. "Sunagumo" was actually used in the TV series as a derisive nickname Falco gave him during battle, but the character himself is literally nameless and most fans simply refer to him by the nickname Falco gave him.
SPOILER for chapters 79 and 80 of the manga: fetus!Envy for... foetus-shaped Envy.
Hagaren - The whole series, whose complete Japanese title is Hagane no Renkinjutsushi (The Alchemist of Steel).
Ho-Ho Papa - Hohenheim. Came about due to the difficult spelling of his German name. Ironically, in the manga his original name is Theophrastus Bombastus Van Hohenheim, but it is shortened to just "Van Hohenheim" because the person who named him (Father) thought he was too stupid to remember it.
Also spelled Hohopapa, and also called simply "Hoho".
Note than in Hiromu Arakawa's official Yonkoma for the anime, Sloth calls him "Hoen" (with a long "o"). Possibly, part of the reason why he isn't nicknamed "Hoho" in Japanese is because it actually means something ("cheek" among others) in Japanese.
Hoju: Hohenheim's late first son in the anime, whom he tried to resurrect, with the result that he created Envy. Short for Hohenheim Junior.
Moofy - Wrath of the anime had no name in canon for a time, and gained the nickname from his fuffy hair.
Mr. Monopoly - Since Brotherhood this is officially the nickname of the Silver Alchemist. The resemblance is uncanny.
Palm Tree - Envy, for his wildly spiky green hair
Sexyhobo - Scar. 'Cause he is.
Scarbro - Scar's unnamed brother.
Shinri-kun or (its anglophone equivalent) Truth-kun - the creepy featureless little guy who lives beyond the Gate of Truth in the manga and introduces himself as "God" or "the Truth").
Shota Mcshadowrape - Pride, aka Selim Bradley.
Tom Selleck with an Eyepatch - Fuhrer King Bradley (Wrath from Brotherhood and Pride from the 2003 anime) because he is.
Ninaxander - A combination name of Nina and Alexander, for the chimera made by Shou Tucker.
The Pimp Suit - The pristine white suit Solf J. Kimblee wears. Because of this, he is occasionally known as Pimp!Kimblee. The same suit is actually a tribute to Alex De Large - so Kimblee De Large works well.
Smooth Criminal or Terumi have recently surfaced from watching the dub, seeing as how Kimblee is, well, a massive Troll like Terumi,
The Eclipse - Berserk reference used by some fans in reference to the events since the heroes have been transported to Father's lair, due to the similar idea of being taken to another dimension and marked as a sacrifice. Interestingly enough, there actually is an eclipse in chapter 104, and it is horrifying.
"Cyclops Army" for the ravenous, one-eyed Mannequin Soldiers/Doll Soldiers (depending on the translation)
"Terminarcher" - In the first anime, Archer, an unpleasant military officer (who only exists in that telling) is made into a suspiciously advanced cyborg after having half his face (or half his head, it's hard to tell) blown off.
And by "half his head", we mean "half of his entire body".
"The anime" — If someone refers to "the anime" they're definitely talking about the first Fullmetal Alchemist anime.
Batshit Ryoma - Ryoma Nagare, specifically in the OVAs, who takes Hot Bloodedness to the point of certifiable insanity. The Armageddon version is the definitive version, and typically the version people mean by "Batshit Ryouma".
Tank Teru: Maho, for also being an aloof big sister of the protagonist who is separated from her and later becoming her main rival, although it's indicated that for Maho, it is a Jerk Ass Facade in order to play the role of the Nishizumi heiress so that Miho can live and do Tankery the way she wishes.
Tank Sumire: Erika, for being Maho's sidekick in the same way as Sumire is Teru's. The two of them also end up missing their chance to shine because of their opponents interfering with their tactics.
Tank Touka for Kei of Saunders. The two even have a slight resemblance to each other.
Kampfgruppe Miho for the protagonist team
Gunner-chan and Loader-chan: Alice's two teammates, named for their respective positions in her tank.
The Haruhi Everyone Forgot - Haruhi Kamisaka: Despite being the main heroine of the show, pretty much no one remembers her or even what the show was about, if it wasn't for Jun's unexpected popularity as a trapon par with Bridget, the show would have pretty much been forgotten by now.
Given her recent chapters having been possessed by a cat-spirit, Izumi has been dubbed 'Izu-nyan' for her apparent attraction to felines and moe appeal while interacting with them (and a pun on Azusa's nickname).
Tako-Musume - The mysterious Tanabe Kozue, who's only appeared once. She wears a conspicuous hat, understands Ika-Musume a little too well... and has Japanese initials that spell tako, meaning "octopus". Hmmmmmmm...
Fluffy or Fluffy-sama - Sesshoumaru; sometimes lengthened to "Fluffy the Terrible", mostly thanks to the fluffy white fur that hangs over his shoulder and trails behind him (itself referred to in Japanese as "mokomoko-san"). Likewise, his recently-revealed unnamed mother has quickly gained the moniker "Fluffette". She is also known as Sessh-mom, for obvious reasons.
Super Shredder - Naraku in his final form, as he resembles the likewise final form of Shredder in Teenage Mutant Ninja Turtles and is considered nigh-invincible.
Inutaisho - Inuyasha and Sesshoumaru's father; a corruption or mishearing of "Inu no Taisho," which is the character's title and means "leader of the dogs."
Occasionally, Inuyasha's father will be referred to as Touga, after a temporary name he received during production of the third movie. It was never made canon, but for some fans it's the closest he's ever come to getting a real name.
And KagoMama or HiguMama or Mama-san for Kagome's unfortuneately unnamed mother.
Sota, Kagome's younger brother, is also sometimes jokingly referred to as "Soda".
Jo2uke - Part 8 Josuke, to distinguish him from the one in Part 4.
Gappy - Also Part 8 Josuke, as his Distinguishing Mark is a small gap between his two front teeth.
195cm組/195cm group - A collective name for Jonathan, Joseph and Jotaro coined by the Japanese fandom based on their mutually shared height.
K or K Project - In the U.S., due to the show's large amounts of Ho Yay, many fans have nicknamed it "Gay Project."
Kagerou Project: The series' main antagonist is most frequently nicknamed Kuroha, due to having no canon name, and since he's an all-blackPalette Swap of Konoha. He is also called "Black Konoha", "Dark Konoha" and "Konoha?", but much less frequently.
Reporn-the series itself or the eponymous character.
Tuna-Tsuna. Apparently the cast is very fishy, since we also have Squalo(Italian for "Shark"), "Octupus Head"(Ryohei's Canon Nickname for Gokudera), and of course Yamamoto's sushi restaurant.
Vongola is Italian for "Clam"
Mukurou-Glo Xinia's owl box weapon that is possessed by Mukuro. A "u" is added to differentiate between the two.
Let's not forget the number/letter code. Usually used for shipping. Example: 5927. D18.
27-Tsuna. Used in canon sometimes. "Tsu" means "2" in Japanese, and "nana" means "7"
59-Gokudera. "Go" means "5" and "ku" is a pronounciation of "9"
96-Chrome. For obvious reasons.
Don't go thinking that these are all of them. The Reborn Wiki has an extensive list if you get confused.
Pineapple-head for Mukuro and/or Chrome, because of their hairstyle. Also "nappo" (Japanese word for pineapple), and "Mini-nappo" for Chrome. Also in Fandom, Mukuro is "Perverted Pineapple" for obvious reasons concerning Tsuna and everybody else he's ever attacked. His assigned number does not help either.
Cthulhu - Gekka, the possibly-ancient flying psychic electric jellyfish that mindrapes people, erases memories, and can change into both a beautiful woman and a gigantic jellyfish that roams the seas destroying random ships.
Boring Germans in Space - Legend of Galactic Heroes, due to one of the sides having noticeable Germanic influence and the fact that some anime fans find it painfully slow-paced.
Legend of Germanic Heroes after said Germanic influences.
Despairs and Nightmares - counterparts possessed by Grace O’Connor, brandished in a somewhat similar way but polar opposite of what Sheryl offers.
Machida - any nameless grunt who does something badass (retroactively appiled to every macross series before frontier), stems from episode 14 when a NUNS pilot referred to on the radio as Machida takes out two red vajra, showcasing the VF-171 in battroid form (the only time we see the standard 171 use a mode other than its plane form), its 7 barrel gunpod and pin-point barrier punch.
Clockiel - Evangelion 2.0 spoiler:The first Angel Asuka fights, with long clock-like limbs, a head that resembles a pair of ticking clock hands, and a hanging orb that resembles a pendulum for a body.
Tunniel - The bony new third angel, named because the trailer showed it in, well, a tunnel. An English branch of NERV, to be specific.
Alternately, Boneliel, for the Angel's skeletal appearance.
Commentary of Evil - The extremely strange commentary of the dubbed version of End, featuring such bizarre quotes as "The true meaning of Evangelion is sex!" Not to mention Amanda Winn Lee singing an off-the-cuff filk of Barnes and Barnes' "Fish Heads".
EGK - Evil Gekijouban Kyoko, for EVA-02/Kyoko's odd and very, very ugly redesign in End.
Rather appropriate as the "Gendo Pose" is also known as the ambassador pose.
GNR (Giant Naked Rei) for the spooky Giant Naked Rei that grabs Unit-01 in The End of Evangelion. GGNR (Giant Giant Naked Rei) refers to the the spooky Giant Naked Rei that falls to bloody chunks at the end of The End of Evangelion.
GNK (Giant Naked Kaworu) for The thing the Giant Naked Rei transforms into to calm Shinji down as he has a panic attack over seeing, well, a Giant Naked Rei. Shinji's ego then collapses, beginning Third Impact.
Harpies - The mass production mecha in 'End of Evangelion''.
Helltrain - The mindscrew train sequences that appear throughout the latter half of the series(For example, when Shinji gets eaten by an angel).
Herr Lorenz - Keel.
Mind Rape - The angel Arael's psychic attack on Asuka. Then again, she does yell "It's raping my mind!" as the beam is in effect (in some translations), and the on-screen text in German does list the word "rape."
Qworu - Rebuild-verse Kaworu, especially his Adaptational Hero incarnation from Rebuild 3.0.
Reiquarium - the tank where Rei's clone bodies were kept.
RIAO (Rei In Appearance Only): The hyperactive schoolgirl Rei from the alternate world scenario in Episode 26.
Kuminator, Kumabots - Bartholomew Kuma and the other Pacifistas, respectively.
Fatsopp - Usopp from the cover arc on 551. Also, the occasional QUALITY screencaps from the anime that gave a similar effect.
Mansopp - Post time-skip Usopp after losing all the weight and gaining muscle.
I believe you mean MANSOPP!
Zolo - Commonly used when discussing things that Zoro did in the 4kids dub as a way of distinguishing him from the original Zoro. For example, "Zolo eats a cookie in the scene where Zoro eats a rice ball".
The Monster Trio, the nickname given for Luffy, Zoro and Sanji, the three strongest members of the crew.
The Weakling Trio, how people describe Usopp, Nami and Chopper. Oda apparently agrees since he had Usopp lampshade this description in conversation with Nami moments after the 2 year Time Skip.
— Usopp: I'm sorry but I no longer belong to the weak trio with you and Chopper.
Megabeard - Blackbeard after stealing Whitebeard's power on top of his own.
Fluffy - An abbreviation of Fake Luffy, an impostor who posed as Luffy.
We also have Fakehats, Flawhats, or Asshats for the impostors as a whole.
Hack - the Haki ability. By extension, Hackers - Haki users.
"Stripey" for the black-and-white striped Sea King that was among the most distinctive of the recurring background monsters in opening animations. During the Fishman Island arc, Stripey even filtered over to the manga when a group of extra-large Sea Kings get summoned to prevent a giant ship from crushing the island.
Homerun-chan - Homura. It was coined in /a/, but quickly gained popularity in Japan as well.
Alternatively, "Homuhomu." This name may have reached Ascended Meme status - one of the items in the Special Edition of Puella Magi Madoka Magica Portable is literally called the "HomuHomu Handkerchief". Interestingly, the source of the nickname appears to come from the Cypher Language in Episode 3.
Widespread enough now that Hideaki Anno used it in a Newtype Magazine interview.
Unlimited Musket Works - Mami's first attack (though they're actually flintlock rifles).
Unlimited Bazooka Works - Homura's More Dakka version.
Chidamari Sketch - the entire series. note Chidamari means "puddle of blood." This was originally from Hidamari Sketch when a character jokingly made up as one of the nicknames of the eponymous rental apartment building. This was promptly applied to this series, due to its content and the fact that character designs for this work was made by Hidamari Sketch's mangaka Ume Aoki.
Condom-chan - Kyouko, the long red-haired girl in the intro because of the... thing she has in her mouth. (Which seems to actually be one of those ice tube popsicle things◊).
Baka Song - The Akane image song "Yasashii ii Ko ni Narenai" ("I Can't Become a Gentle Good Girl"), more widely known by her repeated shouts of "Baka!".
The Nerima Wrecking Crew - Ranma and the other martial artists in the main cast.
The fanfiction Spoiled Brats takes this to its logical conclusion by including a scene with a sign reading: "This residence has been proudly repaired by the Nerima Repair Crew. When they knock it down, we'll put it back up again."
MADMs or Martial Arts Death Machines - Explicitly, the high-powered martial artists in the series, due to the insane amount of damage they can dish out, insane amount of damage they can absorb without injury, astonishing speed (past the speed of sound in some cases), and, naturally, staggering combat skills. Differs from Nerima Wrecking Crew in that the latter can potentially include any character involved in the mayhem; MADMs tend to include only the more "serious" combatants. Of course, precisely "who" those characters are isn't agreed on, but a general consensus would be (of the main characters) the Old Masters and Miniature Senior Citizens Cologne and Happosai, Ranma Saotome, Ryôga Hibiki, and Mousse. They also might add either or both of Shampoo and UkyôKuonji to the selection, as both girls have pulled off feats that are even more impressive than AkaneTendô, though less impressive than those of the guys. Of the various temporary challengers, you have Herb, Mint and Lime of the Musk, as well as Ryű Kumon and, in the anime, Princes Kirin and Tôma.
Ranko - Any version of Female!Ranma that is separate from Male!Ranma, usually an Opposite-Sex Clone. Named after the alias Ranma used when he was hiding himself from his mother.
Some fanfic writers even use "Ranko" simply for girl-type Ranma, instead of the more often seen "Ranma-chan" or "Onna-Ranma".
Kenshin-gumi - The regulars at the Kamiya Kasshin dojo (after The Shinsengumi, the elite feudal police squad of which rival swordsman Hajime Saitou was part before the establishment of the Meiji government)—Yahiko even makes a mention of this nickname early on in the series.
Super Horse - the horse from the Filler episode where he makes a series of spectacular Horse Jumps that would make a motorcycle jealous.
The Four Generals - The "Four Heavenly Kings", the original Quirky Miniboss Squad. Arose from a mistranslation from the early days of the internet, and is incredibly persistent to this day, despite the fact that the correct translation is more common now. There are many fan names like this.
The (Little) Pink Spore (a.k.a. Chibi-Useless, Yam-Head) - Chibi-Usa/Rini. Actually used in the DiC dub of the first anime , later co-opted as a genuine insult by detractors.
"Inner Senshi" and "Outer Senshi" - Fandom terms to describe the major cast division via analogy with the planets. The series never specifically uses the terms, especially because Jupiter is included in the former so they can have a Five-Man Band. Much debate can be had from these terms, especially because the series does in fact give names to two of the groups, and the latter group of four is actually called the "Senshi of the Outer Solar System".
Outer Senshi makes sense as it's simpler to Say Outer Senshi then "Outer Solar System Senshi". The Musicals give the inners the title of "Innner Solar System Warriors" but their offiical title outside that is "Four Soldiers of the Guardian Gods", hence the use of "Guardian Senshi" by some fans.
Asteroid Senshi/Asteroid Quartet/Amazon Senshi: Another name resulting from a fan mistranslation of the Sailor Quartet, who the Amazoness Quartet eventually become in the manga. Since they're only seen and called by name once, many fans had no idea they had a name and coined "Asteroid Senshi" because the four girls are named after prominent asteroids in the solar system.
Silver Imperium Plot Device: The Ginzuishou/Silver Imperium Crystal, due to its Deus ex Machina abilities.
Official Energy Source of the Negaverse: Naru Osaka/Molly Baker, who seems to be attacked by the bad guys an awful lot.
AKA Youma Bait #1. Youma Bait is the derogatory nickname for the youma victims, and Naru is regarded as being the one who attracts them the most.
Sailor Not-A-Planet-Anymore: Sailor Pluto, due to a fall in the planetary rank.
Sailor X: Sailor Pluto, to those who still want to accept her as a Sol Senshi after Pluto was demoted to dwarf planet.
Also applies to Sailor Chi from the manga. X is the greek symbol for Chi.
Dumpling Head/Meatball Head: Usagi/Serena/Sailor Moon, due to Mamoru/Darien mocking her hair.
With fans who like to use the English names, Uranus' civilian name is sometimes changed to Alex (her name in the English translation of the manga), since she is initially mistaken as a boy in the anime (and initially posing as one in the manga), and her offical dub name ("Amara") is too feminine.
The Kougaiji-ikkou and the Konzen-ikkou - Names for two of the three primary foursomes, by reference to the canonical Sanzo-ikkou ("Sanzo's travel partners").
Pippi - So named because of the way her braids stick out. The bossy youkai girl Goku, Gojyo, and Hakkai live with (and are kinda employed by) after her village's Bedouin Rescue Service saves them. She and Goku seemed to have a thing (and kissed), so certainfans desperately hope the fact that she has No Name Given means she isn't important. Barring that, there are epileptic saplings that Goku only liked her because her attitude reminded him of Sanzo, or the way a few wisps of her hair fall in her face subconsciously reminded him of his platonic Forgotten Childhood Friend, Nataku, because Het is Ew.
Parigumi - The members of the Paris-based branch of the Teikokukagekidan Hanagumi found in the third and fourth OVA series. This is more likely a back-formation based on "Hanagumi" than a direct application of this trope.
Pansy Man - Used to refer to Tachibana, whose Alter, while potentially very versatile and awesome, is terribly downgraded because he only ever fights with it with or next to the two major badasses of the show.
Shattered Sword of Balls - Tachibana's, mentioned above, Alter, called "Eternity Eight." One of the things he likes to do with it in combat is form the eight little balls into a sword-like weapon. Unfortunately, when fighting the protagonist, this sword gets punched through and shattered very often. This leads to the, at least in the subbed version, line, "You broke my balls!!!" It gets even worse when this leads him to go on a pity trip about how his girlfriend won't like him anymore.
Abuse-tan = Abiru Kobushi. The name is a play on her name as well as the fact that she is allegedly a victim of domestic abuse as she is always covered in bandages.
Anony-tan = Meru Otonashi. She is called that because she likes to text abusive messages much like Anonymous (4chan) is known to do.
Despair-sensei = Nozomu Itoshiki. This guy is super negative and always seem to find some sort of strange excuse to want to make himself taller.
Evil-tan = Mayo Mitama. This is because not only does she look evil, she does evil things (like blowing up houses and stabbing puppies) and gets away with it.
Hikkikomori-tan = Kiri Komori. Because she is a Hikkikomori (social recluse) after all.
Ji-tan = Matoi Tsunetsuki, the resident stalker. The Ji is a Japanese onomatopoeia sound for staring, which Matoi does a lot (at Nozomu).
"Making Yourself Taller" = Fan term for Suicide by Hanging, which was derived from Fuura's tendency to put a positive spin on Nozomu Itoshiki's attempts at suicide.
Opti-Miss = Kafuka Fuura. She has this disturbing ability to come up with positive explanations for anything that should have a negative connotation to it.
Perfect-tan = Kitsu Chiri. She demands that everything must be done properly and has an obsession with having everything equal.
Schizo-tan = Kaere Kimura due to her split personalities.
Slash-tan = Harumi Fujiyoshi because she is the show's resident yaoi fangirl.
Stick-dog = The term for the at least Once per Episode appearance of a dog with a stick poking out of its butt. This phenomenon is caused by Evil-tan.
Waifu-tan = Manami Okusa. This is because she is married to an older man despite being only a highschool student.
When you consider that the actual names of the characters (with the exception of Kafuka's name) are all thematic (in Japanese, that is) to the characters' personalities, such fan nicknaming could even be considered redundant.
Rat Bastard - Red Impulse, mostly a detractor nickname used by fans disgusted by his parental abandonment and abuse of Ken.
The Space Chicken- Leader X, due to his odd facial design that looks like it has a beak
Purple Doberman on Speed- Berg Katse, due to the huge pointed ears on his mask and his ridiculous fashion.
In the fan community, it was once popular to give the G-Force adaptation the name of "G-Farce", due to it being perceived as inferior to Battle of the Planets and a slight at those fans' childhoods. Eagle Riders also earned the nickname "Evil Writers" due to the bowdlerized nature of the dub.
Waffles — Gopher. Somebody on one of the communities mentioned the multilingual pun, and now...there's 4koma where Gopher is played by a waffle. (Does this make any pairing involving Waffles a Cargo Ship?)
Kakashi's Evil Twin - White*Star (Black*Star's father and leader of Starclan) because he looks just like Kakashi from Naruto.
"Hory Froating Head-sama", for series head honcho Shoji Kawamori no less. This one originated on the Macross World message boards, thanks to a gag picture sent from AnimEigo celebrating the completion of the remastering of Macross — it was of a couple of AnimEigo staffers holding up one of the DVDs as an oversized head of Kawamori looked on, wreathed in a halo.
Kyon-Kun Denwa for the first lines of dialogue during Endless Eight.
Harutards - Harsh name for a Haruhi fan from Fan Haters.
The Trolling of Haruhi Suzumiya - Given to Endless Eight.
The Save the world by Overloading it with fun Haruhi Suzumiya Brigade - a possible English-language version of the hilarious backronym Haruhi gives the SOS Brigade. Ascended when the official English manga and light-novel translations used it.
A later (and obvious) Fan Nickname being Slaves Of Suzumiya.
Bruce Ironstaunch - The fan nickname for a single crowdgoer that gives an arm gesture that is meant to be supportive, but to westerners comes off as meaning "fuck you!" to Rossiu after the latter announces the decision to execute Simon to the masses.
Doombitch - The fan nickname for Yoko, since everybody she kisses ends up dead.
In Latin America, she is nicknamed La Viuda Roja (Literally translated as "The Red Widow")
The Professor - Reite, the group's mechanic/chief engineer, thanks to her limitless skill with machinery, possibly in reference to the character on Gilligan's Island.
Beam Spam McMuppet - The fan nickname for Attenborough, the Gonk gunner of the various Cool Ships of the series, who is a big fan of the tactic. "HASHAAAAA!"
Lulussiu and Spinsimon - Two fan names for Rossiu and Simon after the Time Skip coined from GameFAQs after the in-turn fan nicknames for Lelouch and Suzaku, since both pairs of characters share the same English voice actors and, after the Time Skip, similar actions and relationships.
Palmface - Lunatic, because of the vaguely hand-shaped flame decal on his mask. Kotetsu calls him something of the sort ('palm-head', maybe?) in one episode. It turns into a Funny Aneurysm Moment when we find out why his mask is like this.
Keith Badman - Any evil incarnation of Sky High/Keith Goodman.
Superhero Saturday - Saturday, the day the show aired during its original run.
Tiger & Lunatic - The show after episode 20 thanks to fan speculation that Lunatic, as the only NEXT that still remembers Kotetsu, will team up with him in order to help him clear his name.
The crapsuit - Kotetsu's old spandex Wild Tiger costume that he wears in the first episode and breaks out in the twenty first. Despite the name (which comes from Saito's "and here's the crappy old suit you used to wear" line, he literally calls it a "crap-suit" in the english dub too), the fandom's actually rather fond of it.
King of Moe - Keith Goodman/Sky High, the King of Heroes who just happens to act like a sheltered, virginal Ingenue half the time.
In the audio dramas and other side materials, Barnaby occasionally detaches himself from his default Ice King persona to mess with his fellow heroes (usually Karina) — just for the hell of it. This version of Barnaby is called Trollaby by the fans.
Syaoran Jr., "Syaoran": Tsubasa-kun, to differentiate him from the father who's name he uses until the very last page
The plot is often referred to by many readers as a long string of swearwords screamed at the skies.
What made it worse was having to go through so many name changes as the chapters came out. Syaoran->R!Syaoran->Syaoran Jr./Jr./"Syaoran"->Tsubasa[-kun]. Not to mention the the whole Syaoran/Cloney/Syaoran Sr thing. Thank God the fandom fell into name conventions pretty quick.
MILFBlade - Masane Amaha, single mother and heroine.
AKA Masa-Mune; she's actually called "Masamune-san" ("Mellony" in the Dub) by sleepy Tozawa when they met in the 5th episode (and the nickname sticks). Which gives Rihoko opportunity to cheerfully explain why...
"Book Travels" ("hon no tabibito") and "Hat travels" to shorten out the title
Chichi Kitsune or just Chichi for Tamamonomae: she's a buxom fox spirit who speaks with a Kansai dialect. ("Chichi" is Kansai way of saying "chest" or "breasts", and is even called upon by another Kansai-speaking character, Ken-chan, in the anime)
Season 0 or The Shadow Games - Name often given to the Toei anime version, which is called simply Yu-Gi-Oh!. (The anime most Americans know as Yu-Gi-Oh! is called Yu-Gi-Oh! Duel Monsters in Japan.)
Minigoth - Yugi Muto
Yami - Yugi's "other self", the Egyptian Pharaoh. Oddly enough, the English dub also uses this term and "Big Yugi" for the implied distinction, although canonically, it probably shouldn't be used.
Japanese fans love to distinguish between the Yugis by calling normal Yugi "Aibo", the Dark Yugi's nickname for him, which translates to "Partner" (except stylized and romanized in English as "AIBO"), and the Dark Yugi "Ou-sama" (Japanese for "king").
On top of those, we've got 'Kura, Akefia, Tzroku, Mariku, etc etc etc... It seems everyone has their own personal favorite.
Furthermore, many fan circles will refer to the omote/surface personalities as "Hikari", which means light and contrasts to the "Yami" term.
For those who like to give their favorite characters actual names, we have Florence and Melvin.
Japanese fans also love to refer to both regular and Yami Bakura as "Satoshi," in reference to the fact that their Japanese voice actress, Rica Matsumoto, also plays Satoshi in the Japanese dub of Pokémon.
They also distinguish between normal Marik and Yami Marik by referring to the former as "Namu" (the fake name he used) and to the latter as simply "Marik."
Cabbage - Toei version of Seto Kaiba. Just look at his green hair and you'll know why.
Jellyfish, also for his hair. Add Yuusei as Crabhead and Yuugi as Starfish and the invertebrate trio is complete.
Fianceshipping - The pairing of Judai/Jaden and Asuka/Alexis, named after a Japanese episode in which if Judai won a duel against a tennis player, he'd become Asuka's fiance. He, of course, won but is too airheaded to know what a fiance means. There are also innumerable other names for pairings like this in the fandom.
Principal Awesomebrows - The GX manga's Principal Mackenzie, due to his rather prominent eyebrows.
Plot Device Dragon (PDD): Crimson Dragon, because it literally is a plot device.
Rexposition: Named for Rex Godwin's expositions about the plot.
Rainbow Road: For the special kinds of roads dueled on in episode 26 and 64. A name taken from the Mario Kart series's track.
Little Penis: An alternate legitimate translation for Aslla Piscu, even though the intended translation was Little Crow.
Oxymoron Dragon: Savior Red Demon's Dragon, because its an oxymoron in itself.
Haranimation: For the animation done by Kennichi O'Hara.
Mini-D: Nickname for Sly prior to his official debut due to his resemblance to Divine.
Dark Glass: The blue-haired, left-handed D-Wheeler who teaches Yusei Accel Synchro. An in-series nickname. Also called Racer X.
Robot Shrimp/Robofetus: For the robot thing seen in episode 93 and the fourth opening.
Jack's Wheel of Fortune is starting to be called the Wheel of Misfortune because he crashes or falls off his bike far more then any other duelist in the series. People now have running bets on how long it will take him to injure himself again.
Yuusei is now called "Hobosei" because of his outfit in Episode 116.
After hanging out in the Ark Cradle with Zone and what's happened between them, Sherry's been dubbed "Sin Sherry" amongst fans.
The show itself is 6D's among a lot of fans after Lua gained a Birthmark of his own and Life Stream Dragon.
Japanese Cardgame Batman: Kaito. His character introduction consisted of him diving off of a skyscraper, flying into a building on robotic glider wings, smashing through the window, and dueling a criminal into submission.
Kaito "Flying" Tenjo: Refers to how Kaito always dramatically swoops into a scene on Orbital 7.
Number 96: Dark Mist has been called Buff Mist and Black Muscle after the events of episode 102.
Many of the Zoids themselves are referred to with shortened or cutsie-fied versions of their official names.
Gilvader = Gilvy, Gojulas Giga = Giggles, and so on. Gildragon — a white/blue/gold recolor of the black/pink/purple Gilvader — is referred to as Gildy, or as Mrs. Gilvader due to its "prettier" color scheme.
Besides the obvious "Gungy", the Gungyalado is also known as "Trogdor" after the Homestar Runner chracter that it resembles.
Whitz Tiger Imitate, a recolor of the Whitz Tiger molded in a cheddary orange, is nicknamed Cheese Whitz after the Kraft imitation food product.
On a related note, the sword-armed Savinga included with the Rez Tiger earned the nickname "Sporkvinga"
While Western release names are often used, the Merda is almost invariably referred to by its UK-release name, "Hellrunner", even in reference to Japanese versions. This could be because nobody can actually agree on the proper transliteration of its name (Merda/Merder/Mardar/Muda/etc.) and might also confuse it with the similarily-named Malder. (Or because it's uncomfortably close to the word for "shit" in several Romance languages.) The English-language version of Zoids Saga 2 actually used that name... though that translation was full of other bizarre moments.
The Holotech series (a line of kits cast in translucent plastic) had its own nicknaming convention: the Holotech versions of Zaber Fang, Raynos and Spinosapper became Holokitty, Holobirdy and Holosapper respectively. The Holotech version of Warshark, whose Japanese name is Wardick, is called Holodick (a play on Star Trek's Holodeck) or Holothingy.
The Murasame Liger earned the nickname "Lump Liger" amongst the model-building sections of the community due to the fact that the model came mostly pre-built — ie, a Lump. The Hayate Liger (based on the same frame) was nicknamed "Brick Liger" becuse of its bright red colour - and the fact that the toy ended up looking like a brick.
The Gairyuki ended up as "Gary". The later Gairyuki Shin was often referred to as "Gary Shin", while its new Raiden support unit was called... Spork.
Due to a ridiculous number of customized Zoids based on the Geno Saurer and Geno Breaker appearing in the GBA game Zoids Saga — as well as in fanfiction and online RPGs — all of which share the "Geno" prefix, any such custom is referred to (in some circles, anyway) as a Genothingy.
The last four episodes of the first anime series, Chaotic Century, were known among fans as the Final Four (presumably after a sports term). During its initial run on Cartoon Network, the series abruptly cut off just before the airing of these episodes and started over from the beginning; when this second run reached the cut-off point of the first run, the network aired the last episodes in a two-hour block, explicitly referring to them as the Final Four.
The Berserk Fury's trademark spinning claw weapons are often called "eggbeaters". Its name is also often shortened to "BF".
In-series, the Zaber Fangs, formerly known as the Tigers Team, are referred to as the "Fuzzy Pandas", as Bit doesn't think they're worth the threatening name. This is directly responsible for their last loss in the series.
Anyone named Keiichi, such as the protagonists from Ah! My Goddess and Higurashi no Naku Koro ni, will often be referred in the show and by some fans as K1, which would still be pronounced as Keiichi in Japanese.
The Keiichi in Ah! My Goddess did, at least once, wear a jacket with "K1" monogrammed on it.
"Sentai Filmworks/Section 23 Films" was the result of ADV Films divesting its assets. Because of this, the new entity is often called "Neo-ADV", or sometimes "Zombie-ADV".
Noodle People - The spindly and strangely-proportioned (even by anime standards) character designs that appear in Code Geass, Tsubasa, and Xxx HO Li C which, while (sometimes) good on paper, can be prone to QUALITY shots when animated and are often possessed by people who should probably be more muscular given their physical ability.
Go Nagai has often been referred to in certain circles as "Uncle Go". The same goes for Ken Ishikawa, but less often.