Curse Quest: Minerva Wiseclaw, one of the few competent characters is a skilled shot being able to take down an owl-bear in a few seconds. She is very passionate about law and is currently on a quest to save a small village's government from falling apart.
Nearly every educated Spark (mad scientist) in Girl Genius qualifies for this trope, including the protagonist, Agatha. Not only can they build death rays and turn even the most innocuous of mechanical items into death traps (such as a merry-go-round that can level a small town), but they are generally shown kicking butt with their bare hands (and feet) as well as with less sophisticated weapons, such as giant wrenches and rapiers. And brooms! Badassness depending on anger level seems to be common among sparks.
A recently-introduced character, Jorgi, is a Jägermonster with a background in academic philosophy. There's probably some overlap with the Genius Bruiser here, but he was a bookworm first.
Boris Myshkin-Dolokhov is Baron Wulfenbach's right hand man and chief administrative secretary. Dolokhov isn't a Spark, but he is brilliant, ruthless and a supremely competent organiser. He was originally a librarian, until his former master gave him an extra pair of arms, along with enhanced strength, speed, balance and co-ordination, in order to turn him into the perfect juggler. However, these modifications are also highly useful in a fight. Boris is more than a match for most Jägermonsters in hand-to-hand combat.
Some of the librarians of the Incorruptible Library probably qualify since their Acquisitions Department is apparently heavily armed.
In a way, all five Agents of the Realm qualify, as they're in college, but Paige stands out as a straight-A student who won't let this whole Magical Girl business get in the way of her marks.
Uni-Man. He comes from a planet whose collective intelligence caused a mutation in the planet itself, and is himself a brilliant scientist, currently developing powerful weapons for Axe Cop and his team. However, when Dr. Stinky Head steals his unicorn horn, Uni-Man interrupts the ensuing carnage to reclaim his horn...and then this happens.
Thus this possibly being the most popular ship in the series, aside from Vaarsuvius/Belkar
Zaebos from Earthsong is a member of the elite Haven Guard, and the librarian.
Schlock Mercenary has the relatively short and scrawny Kevyn "I am not a mad scientist" Andreyasn, who habitually wears a 13.75 kiloton antimatter bomb as an epaulet, and a less powerful, but shield-piercing one as another. He's also sometimes been enhanced with nanotech that allowed him to punch through a tank.
Also, Para Ventura (when she doesn't freeze in fear) and Doctor Bunnigus, and Ennesby, and probably a few others.
Colin from Goodbye Chains. Attended MIT with enough engineering skills...to blow everything the shit up. Oh, and guns. Can't forgot those.
Dexter from Powerpuff Girls Doujinshi is able to fight on even terms against the Powerpuff Girls with his robot backpack. Also, in later chapters he fights in hand to hand combat against his rival Mandark.
bookwyrms is about some female students in a magic academy who work in its library in retrieving ancient lost tomes. To quantify their power, the demigoddess isn't the strongest one (despite displaying Hercules levels of might)
Ayanah from Pawn. A physically weak scholar type, she uses her considerable smarts to traverse a legendary dungeon that claimed the lives of mighty warriors, stops the demon guardian from killing her by reciting an obscure demon law, beat said guardian by challenging her to a game she knew the demon knew nothing about, and effectively enslaved said demon with a kiss.
Bob of True Magic. He later threatens somebody whilst the sword's still in the book.
Rose from Homestuck is constantly teased about her reading material by the other kids, which is heavily weighted on the goth and fantasy side of things. Upon entering the Medium, though, she uses that knowledge to become a powerful witch, or something very like it.
Zokusho Comics: Jack's a mage and apparently plays chess quite well. He also sets people on fire.
Underling: Lazarus uses physics and chemistry to deter some pursuers.
Billy Thatcher from morphE wears an argyle sweater-vest and is in line to become the next world chess champion. He has also awoken as an Obrimos mage with control over all the elements and the very ebb and flow of magic. His genius, imagination and strategic thinking applied to those abilities make him the strongest mage of the seedlings by a decent margin.
Wapsi Square has this with Monica and Katherine, both working as anthropologists in a museum. Phix and Nudge are both librarians and could easily qualify as "Cthulhu Bookworm".
Whither has Finn, an unassuming bespectacled Magic Librarian, who embraces the powers bestowed on him in order to save the world (or maybe two). Even before declaring himself "not helpless" he was prone to stunts like defending his companion from a wolf. Using a pocket knife.