Brains and Bondage

""My thoughts ran to Rousseau and Swinburne, both masochists, both geniuses, suffering their mistresses' cruel lashes even as they cried out for perfect enlightenment. Perhaps the body is not our being's basest part after all. Perhaps it is the royal road to knowledge.""

- Presley Abbott, The Oxford Girl

In fiction, people who enjoy BDSM have a tendency to be intellectuals. (This correlation may have some truth, one survey found 20% of practitioners have post-graduate education.) Thus, an interest in BDSM can be used to underscore the character's intellectual side - making Brains and Bondage a mostly "positive stereotype" likely to be used on protagonists and other sympathetic characters.

However, it can also be used as a way to establish a villain as Wicked Cultured. This easily drifts into the Bondage Is Bad kind of Unfortunate Implications, unless counterexamples are provided or the Safe, Sane, and Consensual trope comes into play.

In some works, Brains and Bondage will take the form of waxing poetic about pain or submission. In some Anti Intellectual works, it will instead be used as a blunt tool to make intellectuals look bad by invoking prejudice to make them seem "abnormal".

See also Casual Kink.

Anime & Manga

 * Nana of Nana to Kaoru is basically a female ace - on the student council, athletic, beautiful and a top student. When Kaoru's mother confiscates his bondage stuff and hands it to her for safekeeping—well, we won't spoil it. Suffice to say she finds that bondage clears her head like nothing else because she can step outside what everyone thinks she should be, and as a result her grades go up. Brains + bondage = More brains?
 * And Tachibana, the sex shop owner and, went to graduate school at Todai, the most prestigious university in Japan.
 * Ruby from Rosario + Vampire is The Smart Guy of the Newspaper Club, has extensive knowledge of various monsters and forms of magic, is a capable strategist, works as the direct assistant to the school's board chairman, and is a blatant masochist.

Comic Books

 * In Lucifer, the character Lady Lys tends toward philosophical musing when it comes to pain.
 * For the record, she is a demon and pain harvested from human souls and refined into a powder-like substance is a powerful narcotic for her kind; it's both the main currency and the most common form of recreation in Hell - the actual torture is just a job for most demons.
 * In Global Frequency one of the organization's top scientific consultants is never shown out of his gimp mask.
 * When 355 sends Yorick for therapy in Y: The Last Man it turns out that the process is basically an extended BDSM session with the therapist.
 * In Sin City, most of the female assassins of the Colonel's Guild are into S&M in one form or another. They are all very intelligent, battle savvy women. One of which, is a genetics expert.
 * The Beef Boys from Wildcats 3.0 are never seen without their bondage gear, and the one who speaks (the other always has a ball gag when seen) is very intellectual.

Fanfic

 * A recent fanfic reinvention of Star Trek: Enterprise features as science officer a Professor Polly Partridge, who... Well, just YES.
 * There is at least one Live Journal community devoted to Snape bondage fic.
 * This is not an uncommon characterization for Team Fortress 2's Engineer in Fanfic.
 * Not to mention the Medic.
 * Almost any Harry Potter fanfic where Hermione suddenly "develops" over the summer. Evidently, acquiring boobs also makes her a sex maniac with a love of bondage.
 * There's an awful lot of Heroes fic in which Mohinder is involved in BDSM, mostly as a sub.

Film

 * Severin in Shortbus.
 * Edward from Secretary.

Literature

 * Gravity's Rainbow includes a character expounding on the virtues of "sado-anarchism."
 * The End of Mr. Y has a measure of it. The heroine is every bit the brainy academic stereotype... and she likes to be bound during sex. Kinky.
 * Kushiel's Legacy is made of this trope. Terre D'Ange is by and large highly accepting of any sexual kinks, and while there's less talk among the general public about the S&M practices, they're also considered sacred. This view is magnified exponentially by the main character, who experiences pain as pleasure (the mark of her patron god). She is a high class prostitute, and engages in a wide range of masochistic sexual encounters. Many of these are portrayed as loving, cleansing, or just downright fun. The negative BDSM scenes are a result of true malice on the part of her client, and are portrayed as perversions of the kink, rather than the entirety of it. Moreover, Phedre is extremely intelligent, and the books often wax philosophical on the nature of pain, pleasure, and sexuality.
 * Tarl Cabot of Gor is a Professor on Earth. Unsurprising, as he is a Marty Stu Author Avatar.
 * Vishous of the Black Dagger Brotherhood is a sexual dominant. It's not until the end of his book that he allows himself to be the one tied up and caned.

Live Action TV
"Doctor: Why would you even have handcuffs? River Song: Spoilers!"
 * Dr. Chase from House is a brilliant surgeon who turns out to know the Dominatrix whom one patient has been seeing - they used to hang out at the same BDSM club.
 * Lady Heather on CSI appears to be an intellectual match for Grissom, eventually getting a degree in psychology.
 * Abby on NCIS.
 * As well as another case where the boyfriend was suspected, until he was found tied and gagged. Quite the alibi.
 * In one episode of Castle the victim is a doctoral student who was a dominatrix. Her boss at the dungeon was a former lawyer.
 * Chuck and Blair are considered to be the most intelligent charactersd in Gossip Girl, and they have a lot of fun.
 * Dr. Charlotte Lewis, Sawyer and (hinted) Dr. Juliet Burke in Lost.
 * In the season, Juliet is living in the village with her live-in boyfriend Lafleur . One evening they get a unwelcome visitor . Lafleur beats him up and asks Juliet to get some ropes to pacify him. Without hesitation, she turns to the bedroom. Of course. Where else would she be keeping the ropes?
 * In episode eight of the sixth season, Sawyer is on a date with Dr. Charlotte Lewis. When she says she's an archeologist he asks her if she's like Indiana Jones. When she says yes, he asks her if she have a whip. She smiles and says "maybe". One minute later into the episode they are naked in bed. Charlotte says "Wow. Not bad, considering we didn't have that whip", and Sawyer replies "Bring it next time". Both lines said while cuddling, and said in a very friendly tone of voice.
 * Worf and Dax in Star Trek: Deep Space Nine frequently end up in medical during the middle of the night with dislodged limbs and broken bones. While Worf is more of a highly traditional Proud Warrior Race Guy, Dax is a scientists with literarily several lifetimes of experience first, and treats klingon martial arts just as a sport. It's not explicitly said how they did it, but they certainly like it rough.
 * A lot of Klingons enjoy the rough stuff. On the same morning after Worf and Dax's first night together, Quark and Grillka also showed up in the infirmary with similar injuries. Data even once mentioned that in Klingon culture a broken clavicle during sex is considered a blessing on the future marriage.
 * But that's OK really because Klingons have a spare set of clavicles (don't ask how that works) along with redundant spares for almost everything, up to and including higher brain function - it's when they get involved with another species that problems occur.
 * In the Dollhouse episode "A Spy in the House of Love", Echo is first shown imprinted with a dominatrix personality, and waxes philosophical to Boyd that it's about trust rather than pain.
 * Implied in Doctor Who with the Doctor and Dr. River Song.

"Angel: "What, we handcuff ourselves together? Who do we know that has handcuffs?" Wesley: "Well, I--" *pauses and looks uncomfortable* "--wouldn't know.""
 * Probably skating the line here, but in Farscape you have Wicked Cultured Magnificent Bastard Scorpius who really has a thing for black leather and masochistic tendencies. Yes that way. However, this being Farscape, there are a lot of very intelligent people/aliens enjoying really kinky stuff. There is a reason it's been described as an American man's descent into the Australian BDSM scene.
 * Scorpius isn't a stretch at all. The first (and only, IIRC) time Scorpius and Sikozu are...intimate...onscreen involves Sikozu sitting on Scorpy's lap while he wraps a rope around her neck. Yeah.
 * In the episode "Crackers Don't Matter," the mental clone of Scorpius implanted in Crichton's brain (It Makes Sense in Context), which had been previously encouraging him to slaughter his shipmates, advises him instead to tie Chiana up and " save her for dessert."
 * Hinted at in Angel with Wesley, who has Encyclopaedic Knowledge of demonology. In episode 2.20, we get the following exchange (while researching how to keep together while going through a dimensional portal):

"Sherlock: A power-play with the most powerful family in Britain. Now that *is* a dominatrix. Ooh, this is getting rather fun, isn't it?"
 * In Sherlock, a modern day version of the Sherlock Holmes canon, Irene Adler is a dominatrix who caters to the rich and powerful, using her "access" to gain sensitive material for blackmail and leverage. She's also, in every sense of the word, the only one to ever beat Sherlock Holmes, and much more thoroughly than in the original story.

Video Games

 * Vagrant Story: It's not quite clear why, but about half of the cast is walking around in BDSM gear. And spouting faux-Shakespearian dialogue.
 * A throwaway line from Tales of Monkey Island hints that Elaine (typically the franchise's Only Sane Man) enjoys being tied up (but not for too long, or else she gets cranky).
 * Caster from Fate/stay night. She's a mentally powerful yet physically weak mage who gets off on seeing  tied up and tortured.
 * Kinzie Kensington of the third Saints Row game, who was a FBI computer analyst and hints that she is a regular at a BDSM club that even squicks out the main character. Pierce even points out the leather dominatrix mask she keeps in her hacker cave.

Webcomics

 * While not overly philosophical, Sixx from Collar 6, is a very intelligent and successful hotel tycoon.
 * The Faceless necromancer from Anti-HEROES.
 * In Fansadox, Women Hunt, Mad Satan is the only one capable of running a supercomputer, as he was the one who built it. He also enjoys (and now has the chance to do this extensively) raping and torturing women.
 * Anna in Birthday Gift.
 * Clarice of Girls with Slingshots works in a porn store, is a dominatrix on the weekends and has a Master's in Library and Information Science.
 * Equius in Homestuck is a play on this, as he has a submission fetish and a love of breathplay, as well as a ridiculously flowery vocabulary and an interest in building robots. However, his inability to adjust his stupid prejudices in the face of plenty of evidence shows that despite his book intelligence, he isn't very good at learning from his experiences. It's his prejudice which leads to his eventual downfall.
 * of Katawa Shoujo uses bondage on Hisao in her first sex scene. Her disability comes into play, as

Web Original

 * This list is not restricted to bondage specifically, but it is notable.
 * Ask That Guy With The Glasses, while evil, is however intelligent and has advocated the use of leashes, handcuffs and many other kinky things.
 * The Nostalgia Critic is a Genius Ditz and has big things for masochism, humiliation and strong, dominating women.
 * Speaking of dommy ladies, The Nostalgia Chick's a parodied Brainy Brunette and has told anyone bitching about how Hercules being not like the Greek myths to "stick a ballgag in your mouth and sit in the corner".
 * Sharon, a mechanic from Darwin's Soldiers casually mentions dreaming about handcuffs.

Western Animation

 * Frylock on Aqua Teen Hunger Force, though the "bondage" part only comes up in one or two episodes.