Barbara "Batgirl" Gordon is a bookworm, physically unimposing and underestimated and a literal librarian in her secret identity. She's still capable of kicking the ass of muggers, super-villains and the elite secret agent Spysmasher on different occasions, in addition to being a master strategist with a photographic memory, founder and leader of a superhero team.
Barbara's villain counterpart, The Calculator, was rebooted as one of these. He is even able to outwit Batman himself as a knowledge broker.
Tim Drake, a.k.a. Robin and Red Robin. He devotes his free time to developing electronic gadgets and new chemical compounds for crime-fighting purposes, when he's not actively trying to clone his dead friends back to life. He's been established as being way less agile than Dick Grayson, and Cassandra Cain can wipe the floor with him (the single time he managed to beat her was an extreme case of her Fighting from the Inside), but he's still pretty awesome and can beat Killer Croc while having the flu.
Jason Todd, Robin II/Red Robin II/Red Hood II, was unquestionably the biggest bibliophile out of Bruce's sidekicks and loved school. Even when he was eking out a living on his own in Crime Alley he kept a collection of books, and he was star struck by the library at Wayne Manor. This element of his character was lost in his incredibly inconstant appearances as Red Hood, but had it not he probably would have been rather offended to realize Tim dropped out of school when Jason was never able to graduate due to dying.
Barry Allen, whose powers also come with the benefit of giving him a faster working brain, and were caused by him playing with chemicals. He's one of the most powerful superhumans in The DCU, but he's also a scientist by trade.
Bart Allen of Young Justice is more of a Cloudcuckoolander by personality, but he may qualify for this trope on a technicality for using his super-speed to read every book in the San Fransisco Library in a single afternoon. Since then, his usual 'wing it' strategy has been interrupted by occasional bouts of scholarly tactics.
Justice League of America: Both the heroic and villainous iterations of Dr. Light are physicists which combined with their photokinesis makes them very dangerous opponents.
Justice Society of America: Mr. Terrific is the third smartest man on the planet. He has a knack for having knacks. He also has an Olympic gold medal and six black belts.
And Static is certainly no slouch in this area either. He's a science nerd who happens to kick plenty of metahuman ass. His methods are often very simply effects that are accomplished through impressive knowledge of physics and electromagnetism.
Power Girl is a great scientist, having been taught to understand data and figures very well thanks to an A.I she was raised by. She even founded her own research and development company, Starware Industries.
Supergirl's different Secret Identities (Pre-Crisis Linda Lee, Post-Crisis Linda Lang, Post-Flashpoint Kara Danvers) always look like a glass-wearing, small, physically unimposing, highly smart nerdy girl... who can lift millions of tons with ease.
A certain mild-mannered reporter named Clark Kent can be quite safely stated to be one of the biggest Badass Bookworms of them all.
Vandal Savage, although he deplores fisticuffs, is a Contemporary Caveman with enhanced strength, endurance, and reflexes. He will wreck you if you insist on a fistfight (as many superheroes throughout the decades have discovered).
Wonder WomanVol 1: Byrna Brilyant is a mild mannered stuttering school teacher, who is also a genius level roboticist, very clever chemist, a supervillain who goes toe-to-toe with Wonder Woman and the only known individual to properly subvert a Venus Girdle while wearing one given that she secretly builds a better version of her Powered Armor while wrongfully imprisoned on Reformation Island.
Lucien, the librarian of the world of dreams from The Sandman (1989). When Dream is indisposed and the Furies begin ripping apart the Dreaming, some of Dream's more dangerous prisoners escape their captivity and try to wreak havoc. A few try to do so in the library, but those who tried didn't take Lucien into account.
Thessaly as well. She's a several-thousand-year-old Greek witch who's first introduced as Barbie's nerdy neighbor. She then kills a man, forces his spirit to come back so she can interrogate him via his face which she cut off his skull and nailed to a wall. She then goes into the Dreaming to help Barbie. In "The Kindly Ones" she tracks down Lyta Hall, brews a potion and kills a lamb to protect her. After Lyta comes to she sees Thessaly reading a book and warning her a lot of people are angry about what she did. Thessaly calmly warns her to run, because those people want revenge. And Thessaly's one of them.
Watchmen: Although the second Nite Owl isn't as tough or smart as Ozymandius, he's still a caped crimefighter with enough technical wizardry to build his own crimefighting weapons. He doesn't look threatening and is effectively a comic book geek living out a childhood fantasy.
Films
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.
Wonder Woman (2017): Etta is a very capable secretary for a major wartime office. She might be gentle to a fault, but she isn't opposed to "a bit of fisticuff should the occasion arise" as she points out, if that can help secure women rightsnote . And she actually makes good on those claims to resort to violence when necessary, when she stops the leader of Ludendorff's agents with Diana's sword as his attempt at an ambush goes south for instance, or in the home video stinger, where she uses a beer bottle then a chair to kick the ass of the pub bruiser who came back at Charlie with a gun.
Lex Luthor. He's an avid reader who likes to apply what he's learned to situations in his life. He's also a highly skilled fighter who can beat Green Arrow, the series' most notable Badass Normal.
While Justice League member The Question is more crackpot than bookworm, he does distill this trope into one glorious moment where he nails a guy in the face with a computer monitor just after he's finished using it. He needs to be near threatened by his girlfriend to take her out, rather than review newly taken information from enemies.
In Challenge of the Super Friends, Asian Captain Ethnic Samurai (real name: Toshio Etou) was actually a Japanese history professor in the University of Tokyo before he was turned into a super hero by the New Gods of New Genesis.
Raven from Teen Titans (2003) is very reserved, and spends a lot of her time reading but anyone who seriously pisses her off will have their ass handed to them. Just ask Dr. Light (see the episode "Nevermore.") And if you mess with her friends, you're toast.
just after he's finished using it. He needs to be near threatened by his girlfriend to take her out, rather than review newly taken information from enemies.