The Second Try has Shinji and Asuka becoming milder examples of this trope by necessity, since they had to accumulate and learn the sum total of human knowledge after they're left being the only two humans left alive on Earth, and are pigeonholed into being a civilization of two.
The fic Mortality shows what happens if you really get a mild-mannered doctor like Watson seriouslypissed off. It's NOT pretty. If you really manage to get him pissed, this mild-mannered doctor WILL calmly kill you.
Tara "Green Shield" Strong from DC Nation. Yes, she is a Snark Knight first and foremost, but this is someone who has a Masters at 19, is getting her M.D. by apprenticing under Doctor Mid-Nite, and got her abilities by playing Professor Guinea Pig on herself to try and prevent her crooked boss from taking credit for her work. She's even studying alchemy in order to better keep up with the magical trouble the JSA attracts.
The Pony POV Series has Twilight Sparkle, of course, but there's also Dark World Spike, who's spent the last thousand years as Discord's slave doing pretty much nothing but read to pass the time, from which he's learned a number of fighting techniques.
Harmony Theory: Star Fall is a scholar, magic talent, spy and powerful (by modern standards) mage, able to use her abilities in a fight.
Starr from Pokeumans, despite being seen often in her dorm reading, has certain moments of awesome. The best of which being when they infiltrate Pokextinction's Pine Barrows base.
The Celestia Code features Twilight Sparkle again, as an alicorn. Her approach to dragon negotiation is step 1, offer barter; step 2, carefully applied violence. She also uses applied topography to change a spherical magical shield into a buzzsaw.