Yuri Otani from Alien Nine fits this trope perfectly because she cries frequently, freaks out very easily when it comes with aliens (even seeing them, whether or not they pose any form of threat), the dark, or anything of the macabre (such as in a scene in episode 1 of the OVA where she watches a film on TV, which depicts a man impregnated with a parasitic alien, which then bursts out of his chest). She appears to get worse throughout the course of the series since she joined the Alien Party.
Jun of The Anthem of the Heart is this as a result of her "curse" — she avoids all social interaction because she can barely speak, and if she tries she gets bad stomachaches. She gets better.
Nagisa Shiota is the meekest boy in class 3-E, being very reserved, quiet, and only speaking when he feels he can contribute. This helps him a great deal in hiding his natural skills for assassination, since no one can see him coming. Although he probably developed his meek traits so as to not provoke his mother's Hair-Trigger Temper and violent outbursts.
Manami Okuda is very timid, awkward, and incredibly straightforward, to the point that her first attempt to poison Koro-sensei had her politely ask him to drink it. Koro-sensei helped her develop her language skills and delivery, and she's been slowly but surely coming out of her shell.
Bertolt Hoover from Attack on Titan combines this with being an Extreme Doormat and a Cowardly Lion. He's an exceptional soldier on the battlefield, but his lack of confidence leaves him awkwardly lingering on the outskirts of the group. Unlike most examples, he does manage to have friends by virtue of his Heterosexual Life-Partner (or is he?) being Big Man on Campus Reiner. His shy, meek personality is justified by his Dark and Troubled Pastin that both he and Reiner are Titan Shifters — specifically, the two Titans (Bertolt as the Colossal Titan and Reiner as the Armored Titan) responsible for the destruction of Shiganshina and Wall Maria.
One of the rare male Shrinking Violets who are notButt Monkeys is Yuzo Morisaki from Captain Tsubasa. He's very insecure and was badly traumatised by Hyuga deliberatelyshooting a ball to his face to intimidate him, but Wakabayashi and Tsubasa openly protect Morisaki from possible bullies, and with time he gets over his trauma and becomes a professional GK. In fact, his nickname in the team is "The Courageous Goal Keeper".
Also, Jiang Lihua aka Empress Tianzi. A kind, sheltered Lonely Rich Kid who's trapped in an unwanted Arranged Marriage to a much older Prince from Britannia, the poor little girl can't help but cry often and worry a lot for her guardian and best friend, LiXingke.
C.C. becomes this when she temporarily loses her memories and mentally reverts to a ten-year-old.
Played straight by Sumiko Kobayashi, a shy schoolteacher who once was so timid, her former class was a mess. She tries to be tougher, but Conan and co. unmask her after a short while.
Subverted by Sumiko's co-worker Rumi Wakasa, who looks sweet and unasuming but at times it's all but it's stated (and shown) that she's tougher than she looks, to the point of donning a completely different persona when dangerous people are around her.
Dennou Coil actually has two of these, both male: Denpa, the large but quiet member of the Hacker's Club who is often the victim of his friends' bullying, and Haraken, who winds up on the unfortunate victim end of the plot so often that it makes him something of a woobie.
Hiromi from Diabolo is of this type, to the point of depression.
Yamcha is a male example. He was a caligynephobe; in other words, he freaked out at the sight of a pretty girl. He only got over it when he was forced to spend time with Bulma at the climax of the first story arc.
Alphonse Elric definitely qualifies, to the point where his bolder brother often has to stick up for him. Being a disembodied soul of a ten-year-old child locked in an eight-foot suit of armor that cannot feel or age due to an Emergency Transformation that saved him from an alchemic experiment he and his brother performed that had Gone Horribly Wrong might have something to do with it.
Lan Fan may be a really badass ninja, but she becomes very insecure when she loses her mask. At the end of the story tough, she doesn't seem to need it anymore.
Yukiteru Amano from Future Diary is a male example. Initially, he avoided other people and being involved, describing himself as a 'casual bystander'. He later admits he really did want to have friends, but was "afraid of life".
Meiko Rokudo from Ghost Sweeper Mikami, though she might be a parody of the trope more than a straight example.
Another male Shrinking Violet is actually the lead of Hajime no Ippo. He starts boxing actually to find his inner strength. He's quite the Butt-Monkey.
Later we're introduced to Ippo's biggest fanboy, Naomichi Yamada, who's even more of a Shrinking Violet than him. And anotherButt-Monkey.
Misaki from Hana no Mizo Shiru initially comes across as a fairly standard Tsundere character, but seems to fit this trope in later chapters. From Chapter 6 and onwards his sad backstory and resulting insecurities are revealed in pieces, and he increasingly comes across as more shy and self-conscious. And he fit the "quiet" and "friendless" aspects of the trope all along.
Mallow◊ from Happy Happy Clover is one of Clover's friends who started out as an extremely shy rabbit when she first moved to Crescent Forest and even decided to hide behind Clover's school teacher Professor Hoot when she was a new student. In later volumes, she becomes not as shy as she was in her first appearance but is very sensitive and shy. She would sometimes blame some incident on herself. She would also become Clover's best friend in the third or second volume.◊
The Alternate Universe version of Yuki Nagato from The Disappearance of Haruhi Suzumiya. Also gives us plenty of romance, especially in the spinoff manga "The Disappearance of Nagato Yuki-chan" by Puyo.
Mikuru also has shades of this, as part of her Moe appeal.
Mugi from Hitohira is very much like this. It doesn't keep Nono from dragging her into the drama club.
Yue from Hotarubi No Tomoru Koro Ni barely talks to anyone outside of her step-brother and step-father, she Apologizes a Lot and constantly keeps a low profile. She also feels guilty for what happened with her mother (a failed business venture that swallowed the family's inheritance money), despite having no fault in it.
Mio Akiyama of K-On! is practically the poster-child for this trope in anime. She is tall, has long, black hair, is quiet and kept to herself, is the most level-headed of the group, is only comfortable playing the bass, and is so easily scared that just the thought of a ghost story leaves her huddled in a ball in the corner, shivering. The show is so aware of this that they even give her her own fan-club, including the former student body president, who was so obsessed with her that she began secretly stalking Mio when the time for her to graduate approached.
Himeko Kurusegawa from Kannazuki no Miko. It is implied that her serious lack of self-confidence is the result of being abused by her foster parents when she was younger.
Chrome Dokuro is even more of an example of this trope; her shyness causes her to shut herself in a room, and she doesn't know how to react when somebody is speaking to her. Her not so subtle crush on Mukuro causes her to pass out amidst a battle with a naked giant sucking the life force out of everything.
Also Kozato Enma. Even more so than Tsuna.
Sawako from Kimi ni Todoke feels grateful just for being casually greeted by her classmates every morning. The super popular Nice Guy could never, ever, like her... that has to be her misunderstanding, or her conceit.
Alice of Kiniro Mosaic is extremely shy. When she first appeared as Shinobu enters her house for a homestay, she hid behind her mother—and she's already a middle schooler. Even she's now in high school, she still hides behind Shinobu quite often.
Mimi Usa from Kodomo no Jikan, mainly due to self-consciousness arising from her abusive mother.
Fate was incredibly shy in the first two seasons due to the Parental Abuse she suffered in her early childhood. It's less noticeable in later seasons since she spent 10+ years surrounded by people who care about her.
Einhart from ViVid is a subversion. She is rather shy in normal situations, not helped by the fact that she is the newcomer in a group that has know each other for years. However, she is far more open in matters of combat (Shrinking Violets don't normally go around asking Nanoha for a one-on-one fight). She grows out of it by the time of ViVid Strike! a year later.
Rinne from ViVid Strike! used to be one of these, up until a certain... incident. Ever since then, she's been cold and aloof, though her calling Fuka by her Affectionate Nickname while alone in her room (despite their falling out a year earlier) hints that her original personality is still there (she's deliberately hiding it to avoid being viewed as "weak").
Miyazaki Nodoka fits this trope fairly well, complete with the Hidden Eyes in her early appearances. In the manga this receives a Lampshade Hanging: she has purple hair in addition to having it cover her eyes. Eventually, however, she's developed more, coming out of her shell around Negi and the others. She could almost be described as a subversion; while she has a shy, low-key personality, when push comes to shove, she's ultimately one of the bravest girls and most likely to actually be proactive during very frightening/dangerous situations, managing to keep her cool even when everything is going wrong. Not to mention the fact that, in a series with over 30 potential love interest, she was the first girl to confess to Negi.
And once again with Natsumi Murakami. Despite being an actor in the drama club, she shies away from attention, blushes and stutters when her crush Kotaro is around, and has all but nonexistent self-esteem, partly from being constantly surrounded by women far more developed than herself (especially her roommates, who are also insanely wealthy). She's confirmed to be self-hating when her dislikes include people with red hair and freckles (like her), and she often removes herself from important situations with the excuse that she isn't important enough to be there. Finally, and most telling of all, her artifact turns out to be a legendary-level item capable of completely erasing her presence from other people's perceptions - she is fated by the power of magic to be a Shrinking Violet.
In fact, most of the cast of Evangelion are shy to some degree (even the seemingly outgoing ones such as Asuka or Misato).
Hifumi of New Game is so shy she can barely talk to people directly or even look at them in the eye. To remedy this, her co-workers use the company's instant messaging system to communicate with her at work. There she becomes much more communicative, using lots of emoticons.
Ichigo Otohime of Omujo! Omutsu Joshi has this as a major trait. She is so quiet and reserved that, when she develops hiccups in class, at least one person remarks that it's the first time they'd ever heard her voice. Unfortunately for Ichigo this trait, in combination with a weak bladder that gets worse when she becomes nervous, makes her prone to wetting herself and she wears diapers nearly all the time.
There's always one character in the Pretty Cure franchise that's like this, but Heartcatch Pretty Cure's Tsubomi takes the cake. Flashbacks show that she was so shy (due to poor self-confidence and accidental Parental Abandonment), that her only real friends were flowers. It wasn't until she moved into a new town, met major Genki Girl Erika (and became a Precure) that Tsubomi started to come out of her shell. A major portion of the series, including a story arc, is about Tsubomi overcoming this.
She really doesn't look like this, but Sayaka is extremely shy in regards to her own feelings. And when she's in an emotional corner and her whole world-view starts crashing at the same time... it doesn't end well.
Madoka, the title character, can be seen as one. She's generally more timid than the other cast members, and spends a good portion of the story as a Neutral Female, even for justified reasons. She's also known for Heroic Self-Deprecation and it's implied she wants to be a Magical Girl for this reason. Naturally, the show gives her plenty of Break the Cutie moments. However, it's worth noting that in timelines where she does contract she becomes noticeably more assertive.
Airi from Ro Kyu Bu, is this and she's very sensitive about her height.
Mizore from Rosario + Vampire actually lists "stalking people" as her hobby, because she's too shy to hang out with friends normally. But when Tsukune needs her help, or she's competing for his attention, she suddenly becomes much braver and outspoken.
Ami Mizuno/Sailor Mercury is a quiet and withdrawn Lonely Rich Kid who's always buried in her books, and her peers actually mistake this for arrogance and never approach her. Then comes Usagi Tsukino and pulls her out of her shell, alongside recruiting her for the Inner Senshi...
Hotaru Tomoe/Sailor Saturn. She didn't even have one friend before Chibi-Usa came along because she was so shy.
In stark contrast to her personality in the 90s anime and manga, Rei Hino/Sailor Mars in Sailor Moon Crystal has shades of this trope, especially in her introductory episode.
Yuu, Kuro's Ill Girl older sister, from Achiga-hen. She becomes quite nervous when she sees her sister has brought two guests over, one of whom she knows fairly well, and says that she had considered joining the mahjong club to be with her sister, but felt as though she could not do so. She's also perfectly fine with her friend Arata being chosen as Club President despite Arata being a second year and Yuu being a third year, since it means she won't have to get up on a stage to draw a lot for the mahjong tournament.
Meru Otonashinote Translation: "Soundless" is this trope taken to its parodic extreme: A cute, fidgety girl who can't get a word out of her mouth in the simplest social situation, which doesn't prevent her from constantly sending floods of nasty, abusive, Fourth Wall-breaking SMS messages to her classmates with her cellphone. And what happens when she loses signal isn't pretty...
Kaga Ai. Her entire character is apologizing profusely for being a bother - especially when she isn't. She apologizes for being born.
Ruu, Rii's kid sister, from School-Live! is very quiet and rarely interacts with anyone but Rii. Subverted when it turns out the reason for this is because she doesn't exist, or at least not anymore. Ruu presumably died off-screen however Rii hallucinates that a teddy bear is her.
Aimi Komori is an example of this trope until she puts on her magic eye shadow and transforms into the brash, sexy Classy Cat-BurglarShadow Lady.
Ayumi from Shinryaku! Ika Musume is one. In one episode, she learns to be more confident thanks to a pair of brass knuckles Chizuru lets her borrow, only to have her dad shoot it right back down by saying she's not really doing anything different from the squid girl cosplay she did in an earlier episode.
Megumi in Shokugeki no Soma starts off with no confidence and on the verge of failing out even though the term has just started. Her fear of failure and lack of confidence makes her even more worried, which makes her work even worse than it was. However, her next assignment is with Souma, who helps her regain her confidence. By the end of the training camp, she's also accepted that her niche in cooking is care and attention towards her patrons, not in technical skill or getting everything correct, which boosts her performance enough that she manages to get into the Fall Classic cooking tournament. In her first match, she's intimidated by her opponent and the rather difficult assignment, but holds her ground even when she loses, earning the approval of the school's headmaster in the process. The anime's ending revolves around this character arc.
Sylphiel Nels Lahda from Slayers, is excessively polite, demure, and at times unable to speak for herself, sharply contrasting the main four characters, all who are either more outgoing (Amelia and Gourry), downright boisterous and selfish (Lina), or bitter and occasionally cruel (Zelgadis).
Chrona and Tsubaki from Soul Eater. Tsubaki's Shrinking Violet tendencies make her quite possibly the only character who can handle being Black*Star's partner.
Manami in Sprite: Between Two Worlds (Japanese title Sprite: Manami to Nami) combines this with Split Personality — in her youth, Manami's cousin convinced her to play doctor and other risque games by getting her to pretend to be Nami, an over the top self confident alter ego. Manami grew up to be a textbook Shrinking Violet. When the Alpha Bitch decides to push her too far this combined with her cousin calling out her old nickname causing the outrageously self-confident Nami personality to appear.
Tiger & Bunny: While his superhero persona Origami Cyclone is loud and over-the-top, Ivan Karelin himself is an insecure, timid, very woobie-ish nerd under the costume.
In Tonari no Kashiwagi-san, Kotone's shyness and lack of social skills is what causes people to believe she's an Ice Queen. She also has trouble interacting with Kazuki for a long while, even after getting a little bit familiar with him. However, once people start to discuss anime with her (and it's not in public), she quickly forgets her shyness.
Alessandro of Trinity Blood also qualifies; he is shy and soft-spoken, and has a phobia of loud noises.
Yuki from Tsuritama, a male example of this trope played equally for comedy and drama. The poor kid is so shy it takes him halfway through the series to muster up the courage to so much as talk to some casual acquaintances and overcoming social anxiety is one of the major themes of the show.
Emma from Victorian Romance Emma is like this, which is justified on account of her social station; a girl from beginnings as... humble as hers could never have hoped for a respectable position as a high-class lady's maid, which was fairly high-class for a poor girl in that day, in addition to being literate and owning glasses. Emma is keenly aware of social class and recognizes her absurd luck at having been taken in and educated by Kelly Stowner; she is thusly reluctant to do anything forward enough to jeopardize her career (or hurt William's standing), even if it means turning down the man she loves.
The main character of Wiegenlied Of Green is this in the beginning and for much of the story, having been abused for years by the people in her town for having white hair. Her catchphrase is "I'm sorry for being alive".
Mahiru Inami from WORKING!! is terrified of men. Usually, she simply hides behind corners, stammers, and tries not to look at them. When surprised, however, her first instinct is to scream and punch themacross the room. She also has incredible strength, since her father has been secretly weight training her for years by putting iron plates in her backpack.
Zashiki Warashi from XXX Holic, especially in regard to Watanuki.
Reina's dad from Yandere Kanojo is another male example. This also a deconstruction, beacause his withdrawnness makes him unapproachable by his students (he works at Reina's school as math teacher) makes him mistaken as "scary teacher", "the ones with evil looks", etc, etc while on heart he's probably the nicest character around.
Komasan from Yo-kai Watch is one of the shiest and most sensitive yo-kais, gets scared easily, has a somewhat Friendless Background and adjust to city life harder than his brother, Komajiro. There's also that time when he developed a crush on girl from a coffee shop and even his human form manages to look handsome and shy at the same time.
Cathy is an odd case. Usually, she's the shy girl who is never noticed and afraid to talk to anyone. But she does have another side, one where she dresses in Elegant Gothic Lolita to make her resemble a Cat Girl in order to duel, at which point a far more energetic personality emerges.
As fate would have it, Cathy meets a girl during the Duel Carnival named Dog-Chan (who has the same affinity with dogs as Cathy does with cats) who's an even bigger example of this Trope. Dog-Chan is too shy to face an opponent directly, using her trained (and mean-looking) pet dog Roscoe duel for her, speaking while hiding in a barrel carried on his back to make it look like he can talk.
From Yu-Gi-Oh! R, we get Reiko Kitamori who is so shy she actually would rather run in panic than actually duel. Even her deck is based around walls, designed to distance herself away from an opponent, yikes.
Main character Yuri Katsuki is a very shy and nervous person, especially around his idol Victor before they get to know each other better. His Childhood Friends Yuko and Takeshi state that he was never very good at making friends, and consequently prefers to deal with his problems by practicing at the skating rink or Minako's ballet studio instead of opening up to other people.
Guang-Hong Ji is also shy and soft-spoken, unlike his more outgoing friends Phichit and Leo.
In Shoujotachi Wa Kouya O Mezasu, Uguisu is very timid and minimizes how much interaction she has with anyone at first. And if anyone greets her a little too aggressively, she starts to get uncomfortable around them, looking away while attempting to apologize.