A Crown of Stars: Parodied. When Hikari and Touji fainted after Asuka poked fun at their relationship, Daniel said: “Well, let’s get these two shrinking violets inside”.
Dungeon Keeper Ami has several that wouldn't count except in context. Lishika- a youma with severe Power Incontinence issues -acts a lot like this. She grows extremly nervous when anyone speaks to her. It dosen't help that she has so little control over her powers she once set herself on fire. Ami also qualifies, especially when compared to other keepers.
Neon Genesis Evangelion: Genocide: Keiko is pretty shy, wimpy and mousy. Upon learning that she has been chosen as the Sixth Child, Shinji muses that she reminds him very much of himself back when he first become a pilot... just with breasts.
Surprisingly, the version of Violet in Rise of the Galeforces adheres to this trope a lot less often than the canon version does. She is still somewhat insecure, and her awkwardness around others does show up here and there. However, she becomes increasingly outspoken as the story progresses, and eventually throws the Shrinking Violet shtick out the window completely when the Big Bad makes the fatal mistake of pushing her too far. That's right - she may still be a Shrinking Violet to some degree, but her anger is literally deadly!
Serenity Wheeler from Ultimate Re-Imaginings is depicted like, and so is Andrea Rourke when she's introduced. This is of course taken for a violent turn when she becomes a Yandere intent on killing any perceived threat she finds.
DerpyHooves in We're Gonna Get There Soon, due to fear of being mocked for her eye condition and general clumsiness. It takes Thunderlane, resident Nice Guy and someone already familiar with her, to bring Derpy out of her shell.
In the Axis Powers Hetalia fanfic Seven Little Killers, Canada starts out as this, just like in the real thing; Subverted when he turns out to be the Ax-Crazy seventh killer, just as strong and twice as bloodthirsty as his more globally prominent brother. Then Double Subverted when it turns out that he's only involved with the killers because he's afraid to let go of his older brother's guidance.
In the Fairly Oddparents fanfiction, Never Had A Friend Like Me Norm's lamp ends up in the hands of the shy eight year old, AmandaAdams. She tries to hide in her turtleneck sweater, she avoids any kind of attention, and she generally keeps her eyes locked on the ground.
Twilight Sparkle, of all ponies, became one in Rainboomsand Royalty. In this fic, Rainbow Dash became Princess Celestia's student instead of Twilight, because she was in Cloudsdale when Rainbow's Sonic Rainboom occured. While in the original story, Princess Celestia stopped Twilight's magic surge and made her a student, Twilight's surge went on until she stopped from exhaustion. Having caused a lot of destruction, and having got her cutie mark at the same time, she believed her talent was causing destruction, and she hid herself away, not wanting to hurt others. Rainbow Dash's friendship and fighting her brainwashed brother helped bring her out of her shell.
In the Death Note fic Lies On Light Yagami has shades of this, mostly due to Power Incontinence issues due to his new incubus powers acting up but even before that he was too shy and worried about his image to ask the unique-looking stranger he was interested in out for coffee.
In Mega Man: Defender of the Human Race, due to torture at the hands of Wily, Peekaboo is a very shy, gentle Metool. He's gotten less afraid of things under Roll's care, but is still easily spooked.
Kit Sakura, the Red Ranger from Power Rangers: Shuriken Force. Painfully shy, she's unassuming and quiet, though there's steel underneath when she gives her Rousing Speech to Dare to Be Badass to her teammates.
Chrono Reflect has Standard Rainbow Dash, which is especially jarring considering how her canon counterpart acts. She is Rainbow Dash without her massive ego, also with a friend who abuses her. These two things combined have served to turn her into a timid wallflower. It takes Machine Rainbow Dash, who acts more like her canon counterpart, to draw her out of her shell.
Also, Standard Pinkie Pie, who suffers from anxiety. Once again, this is in contrast to how her canon counterpart acts.
The Differentverse: Per canon, Marble's pretty shy. She eventually starts to come out of her shell, which is represented in-story when she starts to speak at a normal volume instead of whispering all the time.
In Forest of Despair there are two characters that can be described as this, Naoko and Shinichi.
In FREAKIN GENSOKYO we have Maria, a timid witch with what seems to be a tragic past. Definitely not to be confused with Marisa.