"Naruhobo" for Phoenix's appearance in Apollo Justice, from his Japanese name (Ryuichi Naruhodo), HoboPhoenix, Hobonick or Hobonix, for the same reasons.
'Feenie' is Iris's in-universe nickname for Phoenix, but it's been co-opted by the fans to specifically refer to Phoenix as a college student, while the character uses it in reference to both present-day and flashback Phoenix.
Edgey - Edgeworth. Used by Larry Butz in the first game.
Edgey-poo - Used by Wendy Oldbag in the games.
Bratsworth - The younger Edgeworth as he appears in case 4 of Trials and Tribulations and case 4 of Ace Attorney Investigations, from his smug attitude and extremely youthful appearance.
Evil Phoenix - Furio Tigre's de facto English name before the game was translated.
Busty Glory - Fan nickname referring to Mia Fey'sprodigiousassets. Named from a topic at GameFAQs that wondered why Phoenix never asked Mia what it's like in the afterlife, as the potential was right there in all its 'busty glory.'
Dickhead - Daryan Crescend, because of his suggestive hairdo and personality.
Loliziska/Bratziska - The younger version of Franziska, from the same time period as Bratworth.
Japanifornia - The setting of the (English) games, which is an odd mix of Japanese culture and architecture with what's supposed to be a city in California.
"The Liar Hawthorne" or just "Liar Hawthorne" for Dahlia Hawthorne, just to drive the point home that she's evil. For those who like it even more obvious, there's also "The Liar Has-Thorns".
Super Objection - The Objection! at the very end of Trials and Tribulations, when Mia's ghost appears next to Phoenix when he calls Godot out.
"Toasterface" for Godot, because of his visor's slight resemblance to one.
Key Lady was in use for Kay Faraday, before her English name was revealed. Also, Jacques Portsman was often called "Dennis" because it sounds similar to "Tennis", in order to go with the series' Punny Names.
Ace Attorney Investigations 2: As for now, Hakari Mikagami and Yumihiko Ichiyanagi are both known as, respectively, "Judgette" and "Bakahiko" to the western fanbase. Meanwhile, Mari Miwa from case two is "Olga's Mom".
Logicgasm, from Investigations. Edgeworth has an epiphany, and gains several Logic "dots" at the same time.
Athena Cykes from Dual Destinies has gathered names such as Branchhair, Yellow Girl and Artemis for those who either support the theory that she is related to Apolloand the Gramaryes or took special notice of her archery glove and moon-shaped earring. (The moon and archery are both attributes of the goddess Artemis)
While officially referred to as "episodes", the individual chapters of each game are almost invariably referred to as "cases" by fans. Additionally, it is very common for episodes to be referred to in a shorthand format indicating the game and case number. For example, "The Stolen Turnabout", the second episode of the third main series game, is often referred to as "case 3-2", or just "3-2".
Cottagecore Lesbian: Juniper Woods, who wears a straw hat with a sunflower and is often shipped with her friend Athena.
GARcher - Archer, for which the term GAR was originally coined for.
Angry Man Jew - For Avenger/Angra Mainyu, who was sacrificed against his will to become the embodiment of all the evils in the world, and thus save his village in the process. Basically he's Jesus, and he's not happy about it.
K1 or K - Keiichi Maebara. A legitimate translation of his name ("Kei" being the pronounciation for K, and "ichi" translating to "one".) The latter is used in-series as an alternate persona.
Cleaver Girl - Rena Ryuugu, for her iconic weapon.
Droopy, Nurse Droopy, or Droopy-tan - Takano, for her perpetually stoned (and droopy!) appearance.
Mr. Delicious - Kuraudo Ooishi, because of his name's closeness to oishii, which means "delicious". His appearance and drawl don't hurt, either.
Shmion - The collective name for the Sonozaki identical twins, Mion and Shion, due to being Creepy Twins with a tendency to Twin Switch, including an unintended permanent switch when they were younger. So Shion is really Mion, and when she's pretending to be Mion, she's actually acting like Shion! At one point even Shmion gets confused about who she is, although she was under a lot of stress at the time, what with all the killing.
That Psycho Yandere Chick Who Tortures Everyone - Shion as a result of the events of the Cotton Drifting/Eye Opening arcs. Influenced by Never Live It Down.
Kyonichi/Kyuuichi - Yuuichi, for having similar looks/personality and the same seiyuu as Kyon of The Melancholy Of Haruhi Suzumiya. The shared VA is used for a Shout-Out gag in Kanon at one point, with Yuuichi suddenly narrating like Kyon out loud.
Option B - Shin's worstending, which involves Hiroyuki raping Shin, and is named for the choices that crop up late in the route that can trigger it. Thankfully, it's easily avoidable.
Orange - Soutarou, due to , well.. his orange fur.
Sotato - Soutarou again, after a bizarre misspelling in the translation patch during his and Kyouji's beach scene.
Muv-Luv Alternative: "CHOMP", which refers to one of the biggest and most memorable shocking moments in the story. Specifically, Marimo getting her head bitten off by a BETA, with an accompanying, very graphic image to along with it.
Nice Boat - Name for series itself. Just before the planned airing, a RL murder occurred in Japan and it was decided that the murder in the last episode hit a bit too close to home thus it was replaced by a place-holder program titled "Nice Boat". Perhaps by coincidence, the final scene shows Kotonoha on her private boat, cradling Makoto's severed head.
Sucker for Love: Thanks to Markiplier, Nyanlathotep will forever be known lovingly as Big Lady Nyan by fans.
"The Gland", "The Tohno Gland": fan-explanation for Shiki's ability to attract any female, any species. It's pheremones.
Miss Blue (or THE Blue), Magic Gunner: Aoko, whose first name means "Blue Child" in Japanese. Naturally, her hair is red.
Possibly as an extension of the fact that her sister is canonically nicknamed "Red", or "Dirty Red"....only not to her face.
Actually, Aoko's natural hair color is Brown. Ironically enough, Touko's (The above-mentioned sister) original hair color is Blue... which she also dyed Red. (Seems that It Runs in the Family.) And her name means "Bitter Orange Child." Feel free to get confused.
Sensei: Shiki Tohno's nickname for Aoko.
Brainwasher Detective: Hisui, from one of the Bad Endings in Kagetsu Tohya, Tsukihime's "sequel." Her line, "Anata wa hannin desu!" ("You are the criminal!") was misprinted in the game as "Anata wo hannin desu!" ("You, become the criminal!") and the developers liked it so much, "Brainwasher Detective Hisui-chan" was born.
Red Lion, Crimson Red Vermillion: Kouma Kishima in Kagetsu Tohya.
Satsujinki: Nickname for Shiki Tohno, whose Mystic Eyes of Death Perception might become so powerful that he's forced to keep himself blinded once his glasses won't work, in the part joke, possibly-canon "Tsukihime 2: The Dark Six."
Broomstick Girl Magical Amber, Mister Chin, Aproned Devil, Thieving Cat: All four of these are for Kohaku. There's also a fifth nickname occasionally given to her: Nanaya... but only after she loses her memory after nearly killing herself in her path in Tsukihime.
The Serpent of Akasha: Michael Roa Valdamjong.
Capslock-kun: SHIKI. The * REAL* SHIKI, not the fake one who took over his name and identity... AKA Shiki Nanaya.
Sacchin, Badluck Vampire: Yumizuka Satsuki. The latter nickname only applies to her after she becomes a vampire during the Far-Side paths of the game. Bonus: When that happens, she gains Cute Little Fangs.