Okay, stereotypically speaking, in fiction, blondes are lacking the intelligence, redheads are lacking in feminine charm, so, out of the trio, brunettes are all brain. Like the Dumb Blonde the brunette varies quite a bit. They can bashfully hide behind their books, glasses and hair done in pigtails or a bun. Either that or they can boldly use their smarts for their ambitious way. Whichever it is, their knowledge is real—if she's on your side then you can always count on her smarts in a fix. She might be a Hot Librarian, a Hot Scientist, or even a Wrench Wench. If so her Sesquipedalian Loquaciousness and/or Techno Babble will turn people on. And she always has nice, thick, brown locks. What they don't have is strength, like the Squishy Wizard (who might be The Smart Guy himself), as they care more about their mind than their body. That's what makes a Badass Bookworm so interesting, a rare combination.
This trope doesn't mean that blondes and redheads can't be the brains of the outfit. It's just more common for them to have brown hair, especially if they're female, though there are a couple of male examples.
Contrast Dumb Blonde and Fiery Redhead. And, as with both of them, this character can be either good or evil. Make the hair color extremely dark though, and the character borders on Shiny Midnight Black (yet also brainy)
Ouran High School Host Club: Haruhi Fujioka. Though nobody in the host club is truly unintelligent, Haruhi is book smart to the point of being occasionally portrayed as a nerd, and possesses more common sense than most of them. Not to mention that everybody is gay for Haruhi.
Yomi from Azumanga Daioh fits this trope nicely. Excluding Child Prodigy, Chiyo, she's easily the smartest member of the group (with the possible exception of Sakaki).
El-Hazard's Afura Mann, the wind priestess of Mt. Moldune. She's portrayed as the most intellectual of the three and, in The Wanderers series, she has very own library!
Although the Kodomo no Jikan manga can't decide on Mimi and Rin's hair colors, the anime has decided Mimi is a brunette. What shade is still undecided.
Rapunzel from Disney's Tangled— well, she's a natural brunette, anyway.
Films — Live-Action
In the film version of Starter for 10, the character of Rebecca is a brunette and intuitive. She holds various protests and often seen informing the main character, Brian Jackson, of her ideas.
Lanny: My favorite catches were the intellectuals. They'd be the ones in the straight black dresses, severe black hair. Your basic neurotic, eyeglasses, cool jazz, liberal, "I'll fuck any black guy as part of my personal apology for racism in America" type.
The person reading his letter then looks across the room and sees a bookish-looking brunette. And you automatically imagine her doing one thing and one thing only...
Jenny in An Education dreams of getting into Oxford, and she's got the brains to do it. She has a foil in Dumb Blonde Helen.
Emma from No Strings Attached, who studied at MIT, is a doctor in Boston and turned up to a pajama party in actual pajamas in her college days.
Literature
Hermione Granger from the Harry Potter book series is probably the embodiment of this trope in its purest form.
For some reason her hair is more like blonde in the movies, especially compared to Harry who seems to feel out of place academically on his first day.
Harry himself has dark hair and is shown to be pretty smart at things like Defense Against the Dark Arts, as well as getting pretty good grades in general.
Lessa from Dragonriders of Pern qualifies as she is not only the one to figure out Threadfall patterns and trick a Dragonrider into challenging a Lord Holder to a death match, but she also figures out how to save the planet and then does it against the wishes of everyone else involved.
Tiffany Aching of the Discworld books, who read the dictionary for fun when she was a girl, always pestered traveling scholars with difficult questions, and turned out to be very clever and talented for a witch her age.
Jo March in Little Women has thick chestnut hair, "her one beauty" and is a devoted writer.
October "Toby" Daye in Rosemary And Rue is a tough and savvy private investigator who servers both mortal and faerie clients.
Amelia Marsh in Darkness Visible borders on the Shiny Midnight Black end of the spectrum and is very intelligent/educated for a woman of her era. She speaks French, paints beautifully and, to Lewis's surprise, she can play chess. Mrs Emiline Pound also counts, though her hair is going grey. It is her tireless work in the Warden's archives which finally reveals the identity of the traitor among them.
Claudia's sister Janine from Baby Sitters Club is an exaggeration with her Asian and Nerdy ways. Claudia feels bad when she compares herself to her genius sister.
Anji Kapoor, from the Doctor WhoEighth Doctor Adventures, is a genius or very close to it when it comes to economics, to the point of seeming to be a bit of a nerd when you get her started on the topic.
Averted in Percy Jackson: Athena, the goddess of wisdom, is blond and so are her descendants (they have Grey Eyes though). Annabeth, the brains of the group around the title character, is Athena's daughter.
Live-Action TV
Fred Burkle on Angel. She was adorable, sexy, funny, and her high intelligence was a great asset to the "Fang Gang".
Double Subverted with Cordelia in Buffy the Vampire Slayer where Cordelia was shown as an example of the Brainless Beauty, though — after exams it was revealed that she actually had very good grades which she simply chose to hide from her peers, thinking it would make her less popular.
Kaylee, the resident Wrench Wench on Firefly. She had very light brown hair, but it was still brown, and her mechanical genius was definitely a fetish for some.
Simon himself would count, with his fierce knowledge of medicine and ability to organize a heist in one episode.
Inara may make her living with her body, but her brain is no slouch either. She has a working knowledge of many subjects that a Courtesan would be expected to converse intelligently about. She's well versed in human psychology and the arts physical, martial arts, swordplay, history, religion, etc.
Zoe is an expert on setting traps, organizing missions, and leading attacks, all of which were skills she picked up while serving in the military.
Liz Lemon on 30 Rock. Emphasized by the fact that the show's two other female regulars are both Dumb Blondes. In fact, every character ever played by Tina Fey.
The film Baby Mama paired Fey (no, not like that) with blonde Amy Poehler. Guess what their characters' personalities were.
Not quite as overt as the other examples, but Chuck in Pushing Daisies has a great general knowledge and speaks seemingly every language known to man.
Temperance Brennan, Bones. Place your own generic erection euphemism here, I just can't think of a good one.
When you think of it, they're all brunettes.
Abby Sciutto of NCIS. Not that Ziva's any slouch either, with the smart-ass comments and photographic memory. I guess she's more fiery, though. Guess they drew the line at dying her hair red.
Carries over to CSI NY and probably CSI: Miami as well. All the casts have several smart brunettes.
At least in the later seasons, Chloe O'Brian in 24.
Possible subversion in Privileged: Megan, the Yale graduate, is shown as a redhead; however, in the first episode we're told that she dyed it red and we never really learn her natural colour so it's possible she's simply a Brainy Brunette in disguise.
Averted and played straight in No Ordinary Family. Stephanie is a world-class research scientist who graduated from MIT and is blonde. Her nerdy yet attractive sidekick Katie, also shown to be very intelligent, is a brunette.
George from Being Human is described as having a brain like a "planet" and is said by several characters to be able to carry a much more prestigious job than hospital janitor if he wanted.
Carrusel has Valeria, Carmen, and Alicia to a lesser extent. All 3 girls have jet black hair and are good students. Valeria is a talented painter. Carmen is very good with people. And Alicia is very mature and has common sense.
The default player character from A Dance with Rogues has black hair and is really the only character who ever fits the role of The Smart Guy on your team.
Morrigan from Dragon Age, whose intellect is beyond question (though she does seem to spend a lot of it on thinking up more ways to insult Alistair).
Both April Ryan and Zoe Castillo from The Longest Journey series. And the Word Of Godis that the stereotype played (possibly, without realization) a role in their design.
Solid Snake (160-point IQ, speaks six languages) and Otacon (expert programmer, Gadgeteer Genius, creator of Metal Gear Rex) are male examples (although Otacon's hair is more grey-brown than conventional brunet).
Princess Zelda in her only remotely brunette incarnation, The Legend of Zelda: Twilight Princess, is noted by her former tutor to have been an excellent student. She's also the chosen disciple of the Goddess of Wisdom, so it's only logical.
Inverted on The Powerpuff Girls where the red-headed Blossom is the brainy one while the brunette Buttercup is the aggressive spitfire. (Bubbles is still the Dumb Blonde, though.)
Bushroot's Hot Scientist love interest Dr. Rhoda Dendron from his origin story on Darkwing Duck. Morgana the successful businesswoman and scholar counts as well.
Total Drama Island has Noah (book smarts), Courtney (legal smarts), and Alejandro (mechanical smarts).
Played mostly straight with the Kanker sisters in Ed, Edd n' Eddy. May (the blonde) is Too Dumb to Live; Lee (the redhead) definitely has the attitude; and while Marie has blue hair and isn't overtly bookish, she comes up with the smartest ideas.
The Simpsons: An episode's B-plot focused on Lisa joining the debate team and ended up dyeing her hair brown to prove that they didn't take her seriously before, due to being blonde.
On Recess, Gretchen and Spinelli invert their typical hair tropes, as Spinelli (brunette) is firey and Gretchen (redhead) is brainy. Gretchen did have black hair in the pilot, though.
Marilyn vos Savant, listed in the Guinness Book of World Records (at least, at one point) as having the world's highest IQ.
Due to ethnic traits, Asian and Nerdy has almost total crossover with this.
Hedy Lamarr, actress and inventor. Also major-league hottie.
Ellen Page. There's really no need to explain this one.
Audrey Hepburn didn't have much in the way of formal schooling, but she was extremely well-read, could speak at least seven languages fluently, and was a talented piano player.
Emma Watson is enrolled at the Brown University and is rumored to have grades rivaling Hermione Granger's - icing to the cake is that she considers her education more important than her acting career.
