In The Gamer's Alliance, Richelieu wears glasses, looks somewhat unkempt, has a fragile-looking body and spends considerable time reading dusty tomes in his tower. However, when push comes to shove, he shows his opponents exactly why he is one of Alent's most powerful mages.
Rowan Longstripe in Tasakeru is a quiet, even-tempered, philosophical type. He also carries around a gigantic morning star as big as the other characters' heads. And it has spikes.
Tuck and others in The Saga of Tuck are D&D geeks, sci-fi bookworms and math geeks. With a piquant overlay of close arms fighting and covert counterintelligence ops.
If there is a scientist in Darwin's Soldiers (who isn't named Shelton), there is a very high chance they can hold their own in combat.
Sociopathic Hero Jobe Wilkins of the Whateley Universe. Published research papers in biology when he was about ten. Has more biology patents than some entire sections of the United Nations. Just developed a new cure for dysentery. Looks like a scrawny little weasel. Outsmarted a team of trained criminals from the Deville Academy, and then beat the crap out of the one who hadn't yet been infected by the disease Jobe was just researching, in a Crowning Moment of Awesome that was also a Crowning Moment of Funny even though he was giving the villains hideous diseases. In his Combat Final, he nearly beat Punch, who is a TK brick who can knock over a car with one finger.
Half-Human Hybrid Shane Myers from Strange Little Band is one of these. He's generally quiet and unassuming. More interested in his research and family than anything else. He can also kick ass both physically and psychically when he needs to.
MSF High Forum: Joni, sort of. She's not quite badass yet, but she's studying to be a mage... And she has the bookworm part down pat (she has a bookshelf which spans a wall of her dorm room).
Ather City: At first, Nick seems like an annoying nerd who tries to make people scared of him by having better weapons than them. Then he throws a building at you.
Derek the Bard, of Warning! Reader's Advisory—magical librarian extraordinaire.
The Hermit from the Global Guardians PBEM Universe is perhaps the smartest being on the planet. He's read entire libraries, and with an eidetic memory can recall it all. He can just look at you and by taking in the details of your clothing, your stance, and so on can tell where you've been and what you've been up to. And he's a bad guy with teams of assassins at his beck and call, so don't piss him off!
Soul in Saga of Soul is the Junior Goddess of Kick Your Ass. Also, a fledgling scientist.
Twelve year old Tamika Flynn, student in the Night Vale Summer Reading Program, managed to survive the entire week and lead the other children to safety, emerging from the Night Vale Public Library clutching the severed head of the Head Librarian and a blood-spattered sticker chart. Also, she completed Cry, the Beloved Country, which was very advanced for her reading level.
Also Carlos the scientist, who's apparently a bit on the shy, awkward side, but who's very brave when it comes to doing science and generally saving the day. But he's not a hero. He's a scientist.
The antagonists of the fourth arc in Psychronicles literally consists of battle scientists. Kind of justified since they took performance enhancement to a much more advanced level, developed high electricity generating spears, powerful armor and kept it to themselves.
The Number Man from Worm is a bookish, spectacled man who normally serves as a super-accountant. His power over complex math, however, is very versatile; it allows him to see the vectors of incoming attacks, plan controlled demolitions on the fly, wallrun horizontally and shrug off multi-storey drops.
In Lightning Dust, Dr. James Melfton, Klaus' father, is more than capable of protecting himself and others, if necessary; he's actually a very good fighter, believe it or not.
The main character of Polyhistor Academy, Mikelle's spend most of his time in Library, and when he's not got his head stuck in a book, he's usually painting. He's got the body of an Olympic Athelete, is good at fighting, and tends to come out of fights with only the most minor of injuries.
Noriko Null from Beyond the Impossible is five feet tall and without any experience in fighting, but she’s able to wipe the floor with trained assassins armed with machine guns. In her underwear. It helps that she has all the knowledge of mankind downloaded into her brain, including every known martial art.
Most characters in Void Domain are shown reading books on a fairly frequent basis. Most characters tend to have some element of badass to them as well. Zoe Baxter and Eva stand out.