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 extreamly 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.
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, if only because of her being highly Genre Savvy, 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 Were 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.