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.
The main girl from the Dating SimDoki Doki Survival: Sanroku no Mystic, Tsugumi Obinata, is a Shrinking Violet and a Dojikko) (and it's speculated she's an Expy of Sakuno, actually). Same goes to Shizuka Hirose, the main chick from Gakuensai no Oujisama, though this depends heavily on which male you're pairing her up with: she's more shy to some guys, but more open to others.
Shinji is a male version of this in Neon Genesis Evangelion. He's played as a Butt Monkey during the comedic parts that are supposed to lull one into a false security. When episode 20 rolls around, no one's laughing anymore, especially not at Shinji's expense.
In fact, most of the cast of Evangelion are shy to some degree (even the seemingly outgoing ones such as Asuka or Misato). The difficulties of human contact are a major theme of the series.
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.
Mamoru from Shin Sekai Yori is a rare male example. He definitely has the heart and the artistic skills, but is very afraid of the dangers outside the comforts of his home village.
Sakaki of Azumanga Daioh can be best described as a Shrinking Sunflower or Weeping Willow, due to being self-conscious about her size.
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.
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. Currently, 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.
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. 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.
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.
Jacuzzi Splot from Baccano! is so horribly shy and scared of other people that he breaks down into tears just trying to introduce himself.
Cathy from Yu-Gi-Oh! ZEXAL 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.
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".
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.
Massively subverted in Deadman Wonderland, where Minatsuki passes herself off as one when she's actually a sadistic killer. However, her faked personality fits this trope to the T.
Zashiki Warashi from XXX Holic, especially in regard to Watanuki.
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.
Meiko Rokudo from Ghost Sweeper Mikami, though she might be a parody of the trope more than a straight example.
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).
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.
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.
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.
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.
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.
Boa Hancock is as far as possible from being a Shrinking Violet... Until she gets around Monkey D. Luffy, that is, which transforms her into one quite easily.
Coby starts as this. As time passes he remains polite and sweet, but gains more of a backbone... enough to stand up against Admiral Akainu, of all people.
Princess Shirahoshi is this in a huge way, due both the the childhood trauma of losing her mother and then being sheltered for a decade in a tower due to a literally Axe Crazy suitor.
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.
Tamaki in Bamboo Blade is very quiet unless anime or sentai shows are involved. Get her started and she can improvise full presentations well into the night.
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.
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.
Alphonse Elric from Fullmetal Alchemist 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.
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.
There's always one character in the Pretty Cure franchise that's like this, but Heartcatch Precure'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.
Ayumi from Squid Girl 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.
Michio Yuki from MW is a male example prior to the exposure of the titular chemical warfare that loses not only his shyness, but also driving him crazy.
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.
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.
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.
Mimi Usa from Kodomo no Jikan.
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.
Alessandro of Trinity Blood also qualifies; he is shy and soft-spoken, and has a phobia of loud noises.
Alice of Kin-iro 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.
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".