Daredevil: Matt Murdock is a blind lawyer who just happens to be a martial arts master.
Doctor Strange: Dr. Stephen Strange likes to spend his free time in his study, usually in a Levitating Lotus Position about four feet off the ground. He can also take you down with a single spell or a well-placed kick, his choice.
Reed Richards at times possesses this. He punched out Blaastar and Klaw, beat Doom in a one-on-one time travel duel, killed a couple of dinosaurs.... He's done his bit for the cause of badassery.
Doctor Doom is an Omnidisciplinary Scientist first, Tin Tyrant second, Evil Sorceror third, but he is also this fourth. He has trained with the best fencers in Europe, routinely engages in personal combat with superhuman, demonic and even godlike foes (with Power Armor, but he still demonstrates skill and experience even with trained and overpowered enemies), and in one story, with stripped of armour and resources, once actually killed a lion with a single bare-fisted punch.
The Incredible Hercules: Amadeus Cho is the epitome of this trope. When he isn't making SHIELD look like a bunch of fools with his mad hacking skills, he manages to take down foes with pebbles because of his understanding of physics and angles. He isn't called the seventh smartest person on the planet for nothing. And it's an open question among fans whether he's really only the seventh smartest.
The Incredible Hulk: Bruce Banner is the Badass Bookworm you wouldn't want to make angry! Perhaps not 100% applicable because the Hulk is a different personality, but overall they're the same person, and can certainly scrap any of the others.
Although there are plenty of people smarter than him, most famously Reed Richards and Doctor Doom, Banner is one of the most brilliant people on the planet, and in his primary area of expertise, radiation, he is totally unsurpassed on Earth, with even Dr. Doom admitting that he doesn't know as much as Banner does on the topic. When he sets his mind to it very little can get in Banner's way.
Not so long ago Bruce lost his powers (again) because of Red Hulk. Every sign on heaven or earth shows that Bruce is so Badass Bookworm that taking away his Hulk persona can make him even more dangerous. It's easy to forget he turned into The Hulk to begin with because he had a career building super-weapons for the government, which as Banner, he's intelligent enough to use and improve upon.
Bruce:You know, it just now occurs to me that maybe the real reason I became the Hulk... was to protect the world from Banner.
Iron Man: Tony Stark. He kicks ass with or without the use of his suit or any advanced technology, considering Captain America taught him to fight.
Mockingbird: Dr Bobbi Morse, was originally a biologist and SHIELD researcher, until Nick Fury decided she'd make a great spy and trained her. She's since became one of the most badass, if understated, Avengers around.
Peter Parker. Science nerd. Photographer. Spider-Man. Once punched Wolverine through an unbreakable plate glass window to fall to the street 15 stories below when he was mad. The epitome of this trope due to being the first known teenage outcast super hero. He's the master of this trope because, despite being a nerd, he gets all sorts of awesome powers and is a straight up Chick Magnet. Second only to Tony Stark in that area (also a fellow Badass Bookworm), but Parker is the original Nerd Superman.
Spider-man's villain, The Shocker. Smart guy and puts up a good fight. Has updated and improved his costume and blast gauntlets based upon past encounters with Spider-Man. Also one of the most professional villains in the rogue's gallery, having an alright win-loss ratio considering that he fights Spider-Man.
Otto Octavius is a highly trained nuclear physicist and roboticist who is a very dangerous physical threat to Spider-Man.
The Vulture is skilled in the fields of electronics and mechanical engineering which allowed him to create the suit that allows him to fly.
Then there's Norman Osborn, who took a drug to boost his own intellect, becoming insane and super strong in the process. His successors (his son Harry Osborn and Roderick Kingsley, the first Hobgoblin) followed suit.
Ultimate Fantastic Four: Ultimate Reed Richards. His stretch powers were regarded as the suckiest of the four right up to the point where he decided to pitch in anyway. Cue Doctor Doom getting thrown into scenery, Annihilus getting shot in the mouth (with his own gun!), and Diablo getting his Supervillain Lair blown up.
Sage, who explicitly has Awesome by Analysis as her superpower. Combine this with a strong Action Girl streak and you have a badass who will beat you up while explaining what you are doing wrong.
Kitty Pryde. Not only is she an electronics genius as a teenager, but she then gets ninja training from Wolverine and develops her phasing power so that she can hit you whilst she's phasing through somebody else.
Surprisingly Rogue is this as well, when she's not the X-Men's Flying Brick Rogue often spends her off-time curled up with a book in her room. Rogue also shows her intelligence in combat smartly by using her Power Parasite ability to counter foes, one time she took Colossus's powers and figured out she could use it in conjunction with her Flight and Super-Speed to go at terminal velocity and attack her opponent with the force of meteorite.
X-23 (Laura Kinney). Although not a savant or genius-level, she's nonetheless highly-educated, multilingual, and once told Storm she's never lost a chess match. She's also an incredibly skilled fighter and deadly assassin, and Avengers Arena reveals she applies Awesomeness by Analysis and Sherlock Scan to plan how to kill everyone around her immediately upon entering a room.
Transonic from Generation Hope. One of her defining traits is that she, in her own words, "reads for fun". She is also a soldier in Hope Summers's personal army.
Tony Edward Stark from the Iron Man films doesn’t have years of combat training only a few boxing lessons from Happy but Tony still used his technical genius to build a suit that gives him the powers of a superhero. It is through the combination of skill and technology that actually allowed him to be the first person to draw blood from Thanos (the dude who kicked the Hulk’s ass) which earned him the Titan's respect.
Natasha Romanov aka Black Widow, 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 Captain America: The Winter Soldier she truly flexes her brain power by not only providing tech support to Cap but also unlocking a decades old SHIELD base with her smart phone. The Avengers illustrates both sides very nicely: she outwits Loki — a literal god of deception — with the right psychological ploys to fool him into revealing his master plan, and holds her own in the Battle of New York against an extraterrestrial army with nothing but a couple of Glocks.
Loki is shown to be bookish (as seen in The Dark World, fittingly for a younger brother living in his battle hungry big brother Thor’s shadow. And despite not being as strong as his bro, Loki still killed thousands of Frost Giants, curb stomped Captain America in a fight and for a time successfully defeated the Avengers and SHIELD by scheming. Loki is the first real Big Bad of the MCU and proved it.
While they fell to the wayside, Jane, Darcy, Selvig and Ian count considering they fended off an alien Dark Elf attack using nothing but portal technology and a car.
Another villainous example would be Johann Schmidt aka The Red Skull from Captain America: The First Avenger, Hitler’s chief scientist Schmidt was the first human to harness the power of one of the Infinity Stones and create HYDRA an army surpassing that of the Axis powers.
Exceeding Red Skull in scientific evil there is Arnim Zola, who was only a meek assistant to Schmidt in his first appearance but thanks to being integrated into SHIELD managed to do 70 years worth of damage to the Earth by planting the seeds of HYDRA within SHIELD. Not to mention Zola effectively turned Bucky Barnes into The Winter Soldier who ruined hundreds of lives as an assassin, and to add the cherry on top Zola lived to 2014 by uploading his brain conscious to a computer in 1972.
Doctor Strange (2016): Dr. Stephen Vincent Strange M.D started out "humbly" graduating with a PH.D, photographic memory and successful career neurosurgery with his only real shortcoming being his arrogant ego. Which swiftly bites him the ass, as Strange gets his hands crushed in a car accident and crippled for life. Thankfully this leads to Strange putting his intelligence for better use studying magic under the Ancient One, becoming Sorcerer Supreme and saving Earth from an Eldritch Abomination named Dormammu. Also if being a Kung-Fu Wizard physician weren’t enough, Doctor Strange is the only person besides Iron Man to actually hold out against Thanos in Infinity War while the likes of Hulk, Thor, and Captain America were taken out quickly.
Wong deserves mention being a true Badass Bookworm as the Librarian of the magic arts, but it gets better as according to Scott Derrickson Wong is far more powerful than Strange and serves as his Mentor Archetype which is a welcome change from the comics where Wong is a glorified sidekick. Wong proves his badassery in Infinity War where he pulls a Portal Cut against Obsidian Cull successfully dis-arming the alien monster.
As per usual Peter Benjamin Parker aka Spider-Man is a Badass Bookworm, Captain America: Civil War shows that he keeps old computer parts in his room, Spider-Man: Homecoming shows how invested he is in science class and even breaks out of a storage vault by hacking the door. In Spider-Man: Far From Home Spidey makes use of Tony's hologram tec as effectively as Stark himself (much to Happy Hogan's joy). Aside from smarts, Spidey also has the usual superior strength, speed, reflexes, durability and senses which makes him one of the strongest characters in the MCU.
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.
