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: The Magnificent World'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 her very own library!
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...
Hermione Granger from Harry Potter is the cleverest student in her year, and she also is a brunette.
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.
Another Discworld example is Adora Belle Dearheart the city's leading golem expert. She even speaks their language, reputed to be very hard for humans to learn. She's also one of the series' biggest examples of Deadpan Snarker. And this is Discworld!
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 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, can play chess. Mrs Emiline Pound also counts, though her hair is going gray. 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.
The Baudelaire siblings from A Series of Unfortunate Events since they are able to escape from many dangers relying only on their skills and knowledge.
Jane Eyre, the title character of Jane Eyre by Charlotte Brontë, shows us that this trope is at least Older Than Radio. She's an intelligent woman with brown hair, who works as a teacher.
Magdalena Swärd, the female protagonist in "De skandalösa" by Simona Ahrnstedt, is similar to Jane Eyre in both background, personality and appearance. So of course, she too is an intelligent woman with brown hair.
Keladry, the protagonist of Tamora Pierce's Protector of the Small, is described as having mousy brown hair. She's a Genius Bruiser whose favorite subject is math, and her classmates frequently ask for her help. During the dull stretches of managing her refugee camp in the fourth book, she amuses herself with engineering projects.
Fred Burkle on Angel. She was adorable, sexy, funny, and her high intelligence was a great asset to the "Fang Gang".
Wesley, who was also one on Buffy the Vampire Slayer before upgrading to Badass Bookworm.
Speaking of Buffy the Vampire Slayer, the Brainy Brunette for this series is, surprisingly, Xander Harris. Despite the fact that he hides behind a facade of being a goofball and a simple loser, he's actually one of the deepest of the main characters, and is much more talented than the rest of them at not only thinking outside of the box, but ignoring the existence of the box entirely.
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.
Inara may make her living with her body, but her brain is no slouch. 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.
According to the series pilot of Gilmore Girls, Rory Gilmore harbours a long-held dream to study at Harvard University, and it is for this reason she transfers from Stars Hollow public high school to the prestigious Chilton Preparatory.
Carries over to Series/CSINY 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.
As is shown by her running after an armed shooter in 1x07, shooting down a bent copper in her wedding dress in 2x08 and by her disarming a armed criminal at gunpoint and turning his weapon against him in 3x08 she can be just as much a brave Badass as Gene and the others.
Diana from The Secret Circle. She is the smartest one of the core group and often takes the lead because of her smarts and capability. Later on, Cassie seems to take the lead more often alongside Diana as Cassie begins to accept her witch ancestry.
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 gray-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.
Makoto Nanaya from BlazBlue plays this trope under the cover of the paradoxical Dumb Blonde stereotype. Unlike Noel, who has a hard time picking up on material, Makoto has no appreciation for studying and is a notorious goofball and sexual deviant (though to be fair, she keeps her dirtier fetishes to herself). Where this trope applies is that what she lacks in academic smarts (that's Tsubaki's territory), she more than compensates for in practical smarts and common sense, which serve her to no end in her job as an Intelligence officer.
Also, Athena, the Goddess of Wisdom, Crafting, and Battle Strategy.
The Autobiography of Jane Eyre: Jane Eyre is portrayed by a dark-haired woman in this Setting Update adaptation. Jane says she has always been very good at school, loves books and reading and considers herself a smart girl. She's based on a very down-to-earth character.
Velma Dinkley of Scooby-Doo: Throughout her various incarnations, Velma is usually portrayed as a highly intelligent young woman with highly specific interests in science (which in the Scooby and Scrappy Doo series leads her to pursue a career as a NASA research scientist) or merely being very well read on obscure fields, such as ancient Viking writing (as in the third Scooby Doo series The New Scooby-Doo Movies).
Jeanette of the Chipettes is both the brainy one and the brunette in the Chipette trio.
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.
Heather specifically lampshades this in Action where she was looking for new hair and said: "I'm too smart to be Lindsay blonde, but Courtney's hair would be perfect."
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 ending 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 fiery and Gretchen (redhead) is brainy. Gretchen did have black hair in the pilot, though.
T.J. subverts this, as he's quite ditzy when it comes to academics, but is a genius when it comes to his schemes on the playground.
Miss Grotke plays this trope straight.
Mike Chilton in Motorcity. He's a bit more subtle than other examples, but he is a strategic genius from his cadet training. He often relies on his Indy Ploy, however.