Jor-El from Man of Steel. Krypton's chief scientist. Rides a dinosaur through a starship warzone. Goes toe-to-toe with a general bred since birth to fight. And sent Superman to earth a couple of days 'before' Krypton exploded.
Jor-El's computer clone. Manages to come up with the plan to defeat General Zod within mere moments of being briefed on the situation. While taking complete control of Zod's ship. He then deftly frees Lois and Clark both from Zod's custody, and gives Zod a Badass Boast on his son's behalf, followed by a "The Reason You Suck" Speech.
Dr. Van Helsing in Horror of Dracula: vampire hunter and has Dracula running by the end of the film.
Robert Redford's character Joe Turner in Three Days of the Condor, about a CIA employed bookworm who accidentally uncovers the usual Sinister Plot and spends the rest of the film using everything he's learned from his books to evade capture/death/assorted bad things.
In Brotherhood of the Wolf, Grégoire de Fronsac is an 18th century French royal taxidermist, scientist, and soldier. His role in the film is half forensic detective and half ass-kicker. After the torture and murder of his friend, the mellow, charming scientist transforms into a double-sword wielding, war-painted killing machine on a Roaring Rampage of Revenge.
Quorra from TRON: Legacy. When she's not derezzing Clu's mooks, she usually reads books from Kevin Flynn's library, which includes everything from Leo Tolstoy and Fyodor Dostoevsky to Buddhist scriptures and Jules Verne.
Ram from TRON crosses this with Badass Normal and Badass Unintentional. He wasn't designed as a fighter - he was actuarial software for an insurance company. Still, he'd been able to hold his own on the Game Grid against Sark's warriors for nearly the equivalent of a year. He's also the only one who figures out what Flynn is without being told.
Hellboy: Abe Sapien's hobbies include classical music, reading, swimming in demon-infested waters, and kicking trolls in the face. Sure, he doesn't look like much of a badass compared to his partner, but his partner is Hellboy.
The title character, when he's not fighting Nazis and retrieving lost artifacts from booby-trapped temples, Indy earns a paycheck as a respected professor of archaeology.
Likewise, though not to the same extent, his father. The lesser display of badassery seems to be his father's gentler nature and distaste for violence, although he manages to bring down a fighter plane with nothing more than his umbrella and some conveniently located birds.
Jijii from Ichi the Killer. A little old Chessmaster, Jijii manipulates the underworld from the shadows until he's confronted by a Yakuza enforcer, forcing him to whip off his clothes to reveal his impossibly muscular frame, then break every bone in an enforcer's body.
Ling Ling Fat in Forbidden City Cop. A member of the Emperor's personal guard due to family heritage, LLF is actually an inventor and practicing gynecologist by trade, but in the end he uses his cunning and remarkable inventions to outfight the villains.
Richard Kimble in The Fugitive, a quiet nerd who ends up giving the US Marshals a hell of a chase.
Donatello of the Teenage Mutant Ninja Turtles is a geek who loves to invent stuff. Given reason, he can also decapitate bad guys with his bo staff.
Jack Ryan, a former Marine, from The Hunt for Red October. He knows tons of naval minutiae. He is not intimidated by senior officers. He can solve a world crisis. He can guess the moves of a renegade Russian sub captain with almost telepathic intuition. He can even jump out of a helicopter into the freezing North Atlantic. And after all this he remembers to bring his daughter a teddy bear when he returns home.
Sherlock Holmes fits this to a T, being a detective extraordinaire, an accomplished fighter, and a violinist. Doctor Watson does fine all on his own, both a doctor and an ex-soldier.
Ditto (naturally) for Professor Moriarty in Sherlock Holmes: A Game of Shadows; he was a boxing champion at Oxford and more than a match for Holmes. He would have won if he hadn't discounted the possibility that Holmes was willing to sacrifice himself to stop him.
Ghostbusters - They're a bunch of disgraced professors (and one blue-collar joe) sending demons, malicious ghosts, evil sorcerers, and other supernatural baddies packing on a regular basis!
Winston Zeddemore does ascend to this in the 2009 video game, though, where he's mentioned to have gotten his degree.
Arthur from Inception. In addition to being the team's researcher, he's smart enough to figure out how to simulate the sense of falling in zero gravity, and badass enough to pull it off, in a limited amount of time, while fighting off mooks. Again, all in zero gravity.
In Crimson Tide, Denzel Washington plays an academy-trained bookworm who Gene Hackman's seasoned submarine commander deems 'not hard enough'. Denzel proceeds to launch a mutiny, weather a counter-mutiny, and launch his own counter-counter-mutiny, all while battling a Russian sub and trying to avert nuclear holocaust.
Nadia from Pandorum is a biologist who knows some martial arts.
Tony Stark from the Iron Man films has no combat training, but he uses his technical genius to build a suit that gives him the powers of a superhero.
Also Black Widow, who can not only mow through dozens of Hammer security in a whirlwind of acrobatic martial arts in the time it takes Hogan to finally beat down one guy, but she also speaks several languages—including Latin, which there's no practical reason to know how to speak it—and can easily hack through Ivan Vanko's re-programming job on the Hammeroids in minutes, shutting them down without breaking a sweat.
In The 13th Warrior, Ahmed Ibn Fahdlan ("Ibn") is a poet sent into exile as an "ambassador." He's the only foreigner of fighting age in the tent when the witch says the thirteenth warrior has to be an outlander. Then a sequence of events show he's not the soft intellectual he seems to be, having expert riding skills, the ability to figure out a language just by listening to it, and, with some modifications to the design, a deft hand with a sword. And he's one of a few left standing at the end.
In the 2011 film Warrior: Brendan's physics students see him this way when they find out about his MMA moonlighting. This one's based on the real-life history of UFC middleweight Rich Franklin, a math teacher before his fighting days.
The Librarian starring Noah Wyle as a librarian who protects a secret collection of artifacts.
General Henry Knox in The Crossing. Glover (and Washington at one point) mocks him for being fat, and he ran a bookshop before the war. He's also a superb artillery officer whose skill is instrumental in winning the Battle of Trenton.
Sinbad's Andre Kimm from Necessary Roughness. A very large lineman who went to Texas State on a football and chemistry scholarship. He ended up quitting football in favor of academics, and by his third year in college he's teaching classes. He does wind up back on the field, and seems to be very good at what he does.
Charles Xavier is an Oxford graduate as shown in X-Men: First Class, with a doctorate in genetics. He single-handedly prevents the Third World War with some quick thinking and telepathy; he blows up the vessel which was commandeered by the Hellfire Club through a Soviet officer on another warship. Later, he holds a telepathic link in order to immobilise Shaw while Magneto pushes a coin through Sebastian's skull. Charles feels everything, but he doesn't let go of the connection despite the agony he experiences.
Hank McCoy earned his PhD (presumably in engineering and a biology-related field) from Harvard at the age of 15, as established in X-Men: First Class. When he's in his blue, furry Beast form, he's blessed with Super Strength, and in X-Men: Days of Future Past, he's capable of defeating Magneto—not even an adamantium-less Wolverine was able to lay a single scratch on the metal-manipulating mutant.
Victor Frankenstein: As demonstrated by Victor's confrontations with the attackers at the circus and with Inspector Turpin (who is habituated to dealing with hardened criminals), Frankenstein can defend himself in a pinch even though he's a scientist, not a combatant.
Merlin is primarily Kingsman's Mission Control as well as the one in charge of overseeing the training of new recruits. He's still more than able to hold his own against quite a few of Valentine's mooks.
Emperor Palpatine/Darth Sidious from Star Wars. Palpatine is a very intelligent man, oftentimes getting through conflict simply by manipulating others rather than taking action himself. But when he does take action, things aren't pretty. He's also extremely well versed in the lore of the Dark Side.
Ball of Fire has a group of scholars writing a new set of encyclopedias square off against mob thugs to rescue a gangster's moll. One professor even reads a book on boxing moments before the brawl, and after correcting for practical experience vs. theory, mops the floor with his opponent.