7 Seeds has Ogiwara Ryusei, who tends to stick his tongue upward. Likely for no particular reason, he does it when he's joking, thinking... or just because.
Action Heroine Cheer Fruitsdiscusses the use of this trope in Toku, observing that since the principal actors wear face-concealing costumes, body language is their primary form of expression and hero characters are generally given at least one iconic gesture or affectation (the examples given, under heavy Pixellation, are Kamen Rider Hibiki's salute and Kamen Rider Ohja's neck-roll).
Matsuri of Ayakashi Triangle often puts one or both arms akimbo, most commonly with the back of his wrists on his hips, but also with his hands on the back of his neck. He always carries his book bag slung over his right shoulder with his wrist pointed outward. Matoi, Matsuri's mother, makes similar gestures with her arms.
Banished from the Hero's Party: When embarrassed, Rit has a habit of pulling her scarf over her face or otherwise hiding it. In one instance, when Red has been flirting with Rit, he gets her to pull her face out of hiding, revealing her to be hiding a goofily happy expression.
Battle Royale: In the manga version, Hiroki Sugimura has a tendency to tap his nose when he doesn't know what to say. Lampshaded by his friend Takako Chigusa.
Grimmjow comments to Orihime that Ulquiorra has a habit of striking his opponents just below the neck, the same location as his own hollow hole. He speculates that Ulquiorra does it subconsciously and may not even be aware of what he's doing.
Grimmjow has a habit of flexing his fingers like claws whenever he's getting excited about a fight or challenge.
Nnoitra had a habit of sticking his tongue out when excited or cocky. His Espada number was also tattooed on his tongue, so his character tic is also what reveals his rank.
Shinji is introduced to Ichigo's class by writing his name backwards on the blackboard and he tends to do other things (like sitting) backwards too. This relates to his zanpakuto's special ability.
In Bloom Into You, Touko's character in the School Play has a habit of playing with her hair when she's troubled. Her nurse quickly picks up on that, and realizes that her patient's troubled about something, presumably the identity crisis the girl's suffering after losing her memory.
Lelouch is well-known among anime fans for his propensity for dramatic poses, but he seems particularly fond of hand gestures that draw attention to his left eye (the one that holds his Magical Eye powers). A good example of this can be seen in the first opening for the show's second season.
C. C. can often be found noshing on pizza or lying down, oftentimes cradling her stuffed Cheese-kun doll.
Death Note: Pretty much anything L does, Near's hair-twirling and playing with toys, and Mello's maniacal chocolate-eating.
In Digimon Tamers, Mitsuo Yamaki is constantly seen flicking the lid of his lighter open and shut. He's never actually seen smoking though.
In Durarara!!, ShizuoHeiwajima tends to take a small object (like a cigarette or lollipop), throw it on the ground and crush it with his foot when a he gets mad - a No-Holds-Barred Beatdown is about to happen.
Fullmetal Alchemist. Envy has a very distinctive grin, which lets us recognize him when he's transformed into someone.
Ginga: Nagareboshi Gin: The dogs tend to lick their chops whenever they're satisfied or ready for a battle.
Gokusen: The heroine is a Yakuza Princess, and thus while she isn't a Tattooed Crook herself, has picked up the gesture of raising her sleeve to show (nonexistent in her case) tattoos when aggravated.
In Great Pretender, Abbie responds to most suggestions and friendly words by Flipping the Bird. At one point, when the rest of the crew is peeking around a door in a Scooby Stack, she sticks out her middle finger into her place in the stack instead of actually looking.
Kars from Battle Tendancy tends to stick his tongue out as a way to intimidate his opponents.
Jotaro Kujo from Stardust Crusaders will draw his index finger across the brim of his cap before pummelling someone with Star Platinum.
Noriaki Kakyoin from Stardust Crusaders has a habit of licking his cherries while rolling them around on his tongue before eating them. "レロレロレロレロレロレロレロレロ。。。 (Rero rero rero rero rero rero rero rero.../Lick lick lick lick lick lick lick lick...)"
Yukako Yamagishi's left eye twitches whenever she's mad or worked up.
Terunosuke Miyamoto has the Stand, Enigma, which can trap and fold anything in paper, but in order to trap a person he first needs to identify their specific "nervous tic". Obviously, he's scarily good at figuring them out.
Also a bit of Compressed Vice; Josuke's tic, biting his lower lip, was never seen before that fight in the manga. The anime subverts this by having him perform this action multiple times in previous fights.
While much more noticeable in the manga, Giorno Giovanna has a habit of trembling whenever he feels a strong emotion, and it is often the only clue to his emotional state. Giorno trembles most violently in situations involving death, suggesting it may often be a response to Trying Not to Cry.
Narancia Ghirga will stand with his arms out on either side with his head hunched forward, allowing his Stand, Aerosmith, to use his body as a runway.
During Stone Ocean, Big Bad Enrico Pucci develops the habit of listing off prime numbers when stressed, as their indivisibility gives him security.
K: Fushimi Saruhiko clicks his tongue an awful lot. He does it to his subordinates, his superiors, people that annoy him, things that annoy him, situations that annoy him, to avoid answering...the list is endless. He even does it to Misaki, or at least when he's not in his specialmode.
Kaguya places her right hand on her left cheek when her feelings for Shirogane start acting up. This is actually an invoked example since she conditioned herself -Pavlov style- to calm down whenever she did so. It's revealed in supplemental material for the anime that she chose this pose because it subconsciously reminds her of her late mother.
Kei starts stretching whenever she's listening in on her brother, in order to hide her interest.
K-On!: In the anime adaptation, Mio always holds her guitar pick in her mouth and flips her hair back over her shoulder before she starts playing her bass.
Monster: Inspector Lunge's most distinguishing feature is his habit of moving his fingers as though he were typing, which (he claims) helps him memorize information verbatim.
When deep in thought, Midoriya has a tendency to mumble to himself. Those who don't know him well tend to be weirded out by this habit.
Uraraka tends to curl her fingers into paws in order to avoid putting all her fingers on something and accidentally activating her Quirk.
Bakugo tends to bare his teeth at his opponents as a sign of aggression. And he never wears his tie properly.
Aoyama always has a close-lipped smile on his face, even when annoyed or scared.
Iida does strange, robotic hand motions (mainly chopping furiously) when he's trying to emphasize a point or is scolding someone, which emphasizes his role as The Comically Serious.
Jiro tends to twirl her earphone jacks around her finger or touches them together when she's embarrassed.
Aizawa rubs the back of his neck and Shinsou Hitoshi does the same thing.
Momo Yaoyorozu occasionally covers her chest with her arm while in her hero costume.
In Naruto, we have Guy and Rock Lee's thumbs ups, Manly Poses, and Youthful Grins; Kakashi's happy eye-arch; Iruka's blushing and scar-scratching; Sakura shoving her fist in the air; Ino sticking her tongue out; Shikamaru slumping his shoulders; Tsunade biting her thumb; Kabuto pushing up his glasses; Hinata finger twiddling; Naruto and Kushina scratching the back of their heads; Gaara crossing his arms...
Neon Genesis Evangelion: Gendo Ikari's so-called "Gendo Pose": sitting with his elbows on a table, fingers interlaced and hands in front of his mouth (thereby preventing anyone from seeing his expression unless looking from below). Thereby saving the animators from having to draw his lips. Coupled with his shiny glasses hiding his eyes, hiding the lips hides pretty much all chance of reading his expression (not that he's particularly expressive under normal circumstances). This also has the side-effect of making him seem more suspect (in real life, many people will subconsciously cover their mouths when they knowingly lie). Gendo also pushes up his glasses in a fairly distinctive manner when he's done speaking, as if to add a non-verbal "...dumbass" to the end of his sentence.
Morei Nekomata of Omujo Omutsu Joshi has a habit of rolling over from side to side when upset. Chapters from her viewpoint show her doing this when she's discovered some obstacle in her pursuit of Shouta. Alternatively, when she thinks she's pulled off, she shakes her head in a similar manner in her excitement.
Nami playfully sticking her tongue out at someone she's robbed or just somehow screwed over. It also shows up fairly often in official artwork and merchandise.
Klahadore has a rather distinctive way of adjusting his glasses, using the heel of his hand to push them up. Most characters write it off, but his old crewmate Jango understands exactly why he does this: his weapon is a pair of clawed gloves, making the normal methods of adjusting glasses impractical at best and flat-out dangerous at worst. The fact that he still does this is what alerts Jango to the fact that “Thousand-Plans” Kuro is as dangerous as he ever was even after five years in deep-cover-slash-retirement.
The odd little dance Chopper does whenever he's denying feeling pleased with being praised. Eiichiro Odasays it was based on a Real Life comedy routine.
Camie the mermaid's distinctive face fault. It's... hard to describe. Her eyes bug out, her teeth jut out, her jaw seems to unhinge, and her tongue looks huge and hangs out.
Bon Clay has a unique facial expression, a wide grin with one eye squinting and the other wide, which gives him away when disguised.
Zoro usually ties his bandana on his left arm, but when he gets serious in a fight, he'll wear it on his head.
Persona 4: The Animation: Yu has an oddly distinct way of crushing the magical tarot cards used to summon his Personas - he extends his arm out forward, flips his hand so his palm faces upwards, and then crushes the card by making a fist. This is entirely new to the anime, and not present in the original game at all.
Ash sometimes flips his hat from front to back when he gets serious in a battle. He mainly stopped after Johto, but he flipped his hat for the first time in years during the Sinnoh Pokémon League Tournament and later started doing it again frequently in Unova.
Drew has a very noticeable habit of flicking his bangs out of this face. He probably does this about twice an episode when he appears.
Miki and his seemingly random stopwatch usage. He did it so often that fans had asked Ikuhara just why the hell did Miki keep timing things? Naturally, Ikuhara gave one of his infamous non-answers.
Also, the protagonist is an athletic girl who will do random stretches in the middle of conversations.
Sazanka: The protagonist, Tatsuki, often puts a hand on the back of her head while trying to laugh off something. Her doing so helps her best friend, Aoi, see a bruise Tatsuki got from her ex-boyfriend, Keita.
Yamori has a rather unique and disturbing method of cracking his knuckles, a habit he picked up from the human that tortured him. His second-in-command, Naki, does it in imitation of his beloved "Big Bro".
Kaneki has a tendency to adopt the tics of people that had a strong influence on his life. From his mother, he picked up the habit of touching his chin with his left hand whenever he tells a lie to spare someone's feelings. After being tortured for 10 days by Yamori, he picks up the habit of cracking his knuckles when irritated or about to do something violent. Finally, in the sequel, he has begun placing his hand against his ear while deep in thought — a habit borrowed from his best friend, Hide.
Toradora!: Ryuuji tugs at his bangs in a characteristic way whenever he's shy, embarrassed, uncertain, or thinking.
Violet Evergarden has the tendency to nuzzle or even bite objects she's holding, as her prosthetic hands don't have a proper sense of touch.
