Rhinox. He's not only this big burly dude that turns into a rhino, he's also the Maximals' tech expert, very wise and aware of his surroundings, a competent leader when forced into the position, and fully capable of manipulating and out-manoeuvring the entire Predacon force. These smarts carried over after his eventual FaceHeel Turn after his spark took over Tankor.
Megatron is another example, being a huge, physically imposing Chessmaster.
Rampage is a hulking, sadistic, cannibalistic monster who is also an expert in psychological warfare.
Freakazoid! villain Cave Guy is one of the series' stronger and smarter villains, being a large and powerful neanderthal with the mind (and dialect) of a Yale graduate/New Yorker subscriber. (Fans have compared his voice and speech pattern to that of Thurston Howell III.
Farmer MacDonald's gargantuan sons Buford and Cletus. Cletus graduated from Stanford Phi Beta Kappa, and Buford is a renowned nuclear physicist. Jackie's read his books on the subject.
Ratso of the Dark Hand is sometimes very perceptive for Dumb Muscle. Oh, and he used to study theoretical physics before becoming a thug.
Tohru, despite being built like a sumo wrestler and easily capable of tearing a building apart with his bare hands, has been proven to be quite intelligent and is Uncle's apprentice in magic, and has solved many of the problems that have faced the team with simple common sense.
In Justice League, the Ultra Humanite is a criminal genius who has transplanted his brain inside an albino gorilla, further transforming this new body to gain enormous strength. He's still a genius, and in fact, was persuaded to turn against the Injustice League because he felt his talents were being wasted working for Luthor.
Rare case in Jack Fenton from Danny Phantom in that he doubles both as a Dumb Muscle (because he's a Bumbling Dad) and Genius Ditz; his ghost invention works. One episode has also stated he held straight 'B-'s throughout his school years.
Marsala in Exo Squad is this and a Gentle Giant: he is both physically intimidating, like most Neosapiens, and a surprisingly insightful orator and tactician. This also applies to Phaeton and, perhaps, Shiva, the two Neosapien villains who rose out of nowhere and conquered most of the Solar system through cunning strategic planning.
During a flashback during an episode of The Simpsons, a big brawny soldier who is called Ox (short for "Oxford" as it turns out, not a reference to a farm animal) effectively explains the concept of a "tontine" (the funny part was that he spoked like a dumb muscle before he turned out be educated on difficult English):
Ox: Duh, essentially, we all enter into a contract whereby the last surviving participant becomes the sole possessor of all them purty pictures.
Jack Bennet and his adoptive son JD, codenamed Bionic-1 and IQ respectively, from Bionic Six.
Though he starts off more akin to Dumb Muscle, Brock Samson develops into this. This is especially apparent by the end of the third season, where he plays The Monarch and the OSI against each other in order to proverbially kill two birds with one stone.
On the villainous side, Amoral Attorney Monstroso is about 10 feet tall, capable of surviving a beatdown from 21 and Brock, and he's the Guild's undisputed master of the double cross. Capable of screwing over practically anyone with some well placed paperwork.
Sherman Cortez is half of the team's strategic, tactical, and tech support on Hot Wheels Battle Force 5. He uses his math skills to perfectly time his escape from a Death Trap corridor. The time each trap has before activating is faster than any human being should be able to react, let alone do calculations. Sherman is just that awesome.
Robin, of course, has had many of Batman's skills rub off onto him and it gives him an elite deductive mind as well as superb melee combat skills (particularly with a staff). That said he tends to let his brilliance overwhelm him at times and he loses focus on what's really important when he's fixated on a task.
Cyborg is both the team's second physically strongest member (surpassed only by Starfire) and the resident technology expert, qualified to build, modify, or repair anything you can think of. Having a computer built into your head helps.
Slade, who has more than enough combat skill and strength to take on the team 5-to-1 and keep up, and more than enough brainpower to stay on top in terms of gambits throughout the entire show. He rarely needs to directly intervene, but whenever a lot of violence is required he's happy to do it himself.
Megabyte from ReBoot is urbane, intelligent, and the one of the strongests regular character on the show. This makes the rare occasions he goes bestial even more frightening.
Occasional Kim Possible villain Motor Ed is a large, muscular, mullet-haired mechanical genius who even outsmarted Wade at one point. As Wade put it, "He's not as dumb as the hair-cut would lead you to think."
Exile from Road Rovers also qualifies. He's one of the largest and most muscular members of the team and has super strength, but he also serves as the team's mechanic. Several episodes has him fixing (or breaking) some very complex vehicles or electronics.
Thailog is smarter than Xanatos and stronger than Goliath.
Goliath himself is no slouch at this either. Yeah, he's a hulking Proud Warrior Race Guy, but while he doesn't have Xanatos and Thailog's brand of cunning, he's very well-read, perceptive, and cultured.
The aged Hudson. When facing a physically younger and better-armed opponent, Goliath remarks that Hudson can't fight her. Hudson corrects him by saying he can, he just can't win. By drawing out the fight, Hudson ensures reinforcement comes to his aid.
Taurus Bulba is a huge bull who likes to pick up and manhandle both his own henchmen and Darkwing Duck, but who is at the same time a Diabolical Mastermind so clever he's not only running his operations from inside prison but also has a flying base constructed inside it just waiting to take off at his convenience.
Octus from Sym-Bionic Titan. His brain is pretty much an encyclopedia, although standard attacks (kicking, punching) don't phase him and he's shown to be able to put up a fight.
Helga From Hey Arnold!! is already fairly known among her classmates as a formidable bully. She's also a talented writer/poet, and quite intelligent for her age. An unusual case in that she's just a bully who happens to be a genius, as opposed to antagonistic genius bruisers from more action-oriented media.
Shockwave is the creator of cortical psychic patch, managed to reverse engineer the space bridge, and has the technical know-how to create clones from fossilized remains. He's also pretty beefy for a robot, has an Arm Cannon in place of his left arm, transforms into an alien tank, able to survive getting crushed by falling chunks of rock, practically unaffected by any attacks thrown at him, and may have even survived a space bridge collapsing on him. His only weakness is his eye and getting a direct laser blast to it barely stuns him. His creation Predaking also shows signs of this. Even Shockwave was surprised when Predaking transformed into robot mode, revealing that he is sentient. When he speaks, he turns out to be rather eloquent and well-spoken.
Megatron has slightly more brawn and slightly less brains than some other incarnations but is still a very savvy strategist capable of being a frighteningly effective Manipulative Bastard when his madness or arrogance don't get the better of him.
For a heroic example, Optimus Prime is his usual devastating self in battle, but used to be a skilled historical records clerk and proves to be a dab hand at cryptography too.
Boulder, from Transformers: Rescue Bots, while a rescue worker rather than a fighter, is the muscle of the team, the one called on when, for example, a school bus needs to be pulled up from the hole that just opened up in the ground. However, he's also shown to have a surprising amount of brains; his human partner is Graham, the team's engineer, and Boulder is easily able to understand him. They've even started studying together, as Boulder finds subjects such as hydraulic conductivity fascinating.
In the Dexter's Laboratory movie Ego Trip, Adult Dexter is a hulking muscleman with a Badass Beard who can reduce Mandark's robots to spare parts, and he hasn't lost any of his smarts.
Ivy, from Where on Earth Is Carmen Sandiego? is well read and loves the arts. She has also kicked through bolted doors, tackled henchmen with flying kicks, and tosses henchmen who have tried to restrain her with hooks, nets, or lassos.
Popeye occasionally gets in on the act, using spinach to enhance his brain power as well as his muscles when necessary.
Big Macintosh. Easily one of the strongest ponies in the series, he proves his intelligence on more than one occasion — Applejack gets frustrated with his "fancy mathematics" in Applebuck Season, and he knows the therapeutic pressure points for Granny Smith's muscle spasms. To top it off, when "discorded", he became incredibly stupid, acting more like a dog than a pony. Notice that for the Mane Six (with Rainbow Dash filling this trope), the same effect reversed their core personality trait, a.k.a. their very Element.
In the Christmas SpecialRudolph the Red-Nosed Reindeer, there's Yukon Cornelius, a badass Prospector who's always coming up with smart ideas. He gets himself and his two friends away from the Bumble by taking advantage of the Bumble's one weakness ("The Bumble sinks!" he laughs) and he later get the good idea to draw the beast away from Rudolph's parents by telling Hermes to imitate a pig, knowing that it prefers pork to deer meat. He's got the Bruiser part down to a T (Boisterous Bruiser, in fact) able to out-wrestle and tame the Bumble after Hermes de-fangs it.
Zaheer from The Legend of Korra is a powerful and seasoned fighter who looks the part, but also a poetic and spiritually knowledgable man who knows a glod deal about the avatar and the world. Made more obvious by the fact that he's voiced by Real Life genius bruiser Henry Rollins.
Amon/Noatak, as well. Really good public speaker, social leader, and master strategist; expert chi-blocker, prodigy waterbender and psychic bloodbender.
Kuvira, too. Manipulative, charismatic, incredibly intelligent, and has allthe skills to back it up.
In the 2006 revival of Biker Mice from Mars, one of the main villains is Cataclysm, a Catatonian soldier who is huge and burly and also serves as the Dragon-in-Chief to his incompetent younger brother Hannibal T. Hairball.
Garnet of Steven Universe is not only by far the strongest of the Crystal Gems, but she's also the savviest and always knows what to do next thanks to her Seer powers. Lampshaded by Steven in "Keeping it Together":
Steven: Oh. Oh! You're brains and brawn! The whole package!
Mr badger from The Wind in the Willows is bigger than all the other characters (in fact he could pass for a bear). His feats of strength include lifting Toad up with one arm and breaking the bell off a hammer striker (he is also fiece enough to scare off the weasle gang even when outnumbered). And as for smarts he knows latin very well.
Kaeloo: Mr. Cat. He owns many weapons and is highly aggressive, and several episodes (for example, "Let's Play Scaredy Cat") show that he is a skilled fighter. He is also a Gadgeteer Genius who made his own cloning machine and in another episode, he fixed a broken time machine.
B from Total Drama is shown to be both quite athletic and an excellent engineer. It was fairly obvious that Scott had to get him eliminated early.
Duke Phillips from The Critic is a media executive with an evil streak who, we are regularly reminded by the statue out front, somehow formed a broadcasting company from a restaurant, and is depicted with exaggerated, cartoonish physical prowess that starts looking like "physically active middle-aged man", and goes up to things like revealing he broke into Jay's apartment by walking through the wall.