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Pilaf's short stature makes him hard to take seriously as Goku's first antagonist, but Goku is just a tiny child himself at the time.
The Red Ribbon Army was led by Commander Red, who was extremely short. This would turn out to be relevant to why his organization kept clashing with the protagonists in the first place: he was after the Dragonballs himself simply to wish himself taller.
Fullmetal Alchemist: Pride is in charge of the other homunculi and, excluding Envy's true form (which he'll try to not use whetever possible), is the shortest of them.
Probably one of the most dangerous alien targets that the Gantz team had to kill was Nurarihyon, a child-sized old man who was always accompanied by his two monstrous sub bosses, an angry-looking Tengu and a giant dog wearing Heian Era attire, who are several feet taller than him. Nurarihyon had the highest point count out of all the previous targets and was a shapeshifter capable of transforming into a variety of different forms, including a 50-foot giant made out of WOMEN. He was also nearly invulnerable and had Frickin' Laser Beams.
One of the earliest examples in comic books is the Big Man. While his costume made him look like he actually was a tall and heavy guy, he was eventually revealed to be a cringing slender lightweight under his padding and elevator shoes. Nonetheless, he was evidently charismatic and intelligent enough to earn the trust and loyalty of the Enforcers, who helped him take over all the other criminal operations in New York City for a while before Spider-Man exposed him.
Fancy Dan, a member of the Enforcers, is also a rather small man, albeit highly self-confident and possessing well-nigh legendary martial arts skills. He was also charismatic and intelligent enough to be shown running his own criminal gang many years later in the Spider-Girl comics.
Big Figure from Watchmen. Averted somewhat as he remains relatively cool despite Rorschach's digs about his height. His bodyguard is not quite so restrained and suffers for it. In the film, Danny Woodburn turns in an excellent performance in this scene as someone who's trying very hard not to show that Rorschach is leaning on his Berserk Button and almost succeeding.
Joe Dalton from Lucky Luke, the mastermind of the four Dalton Brothers and easily the worst-tempered, is two heads tall.
Scarface - and the Ventriloquist is still a small man compared to Scarface's mooks.
The Dummy inverts this setup, being a small man disguised as a ventriloquist dummy, fooling even his own underlings into believing their boss is an eccentric who insists on speaking through a dummy.
Batman villain, The Penguin, has always been depicted as a small man, sometimes comically so. He is, however, shown to have a good deal of Stout Strength when fighting, and his Mooks, while almost always taller, are often no more physically intimidating than he is. (Exaggerated in the later episodes of the animated series, when the Penguin ran a nightclub and employed a number of leggy dames in snowbunny costumes, he was about the size of a tall child, and even the women looked like titans next to him!)
Nappy Klains, The Napoleon of Crime, "They call you that because you're small and evilly ambitious!" in World's Finest #154. He's short enough to pass for a pre-teen boy with the aid of heavy makeup.
Grigori "Little Greg" Irinescu, The Don of the Vampire Mafia in Top 10, who has to stand on his desk so people can kiss his ring without getting on their knees.
René Goscinny as portrayed by Ach!lle Talon. This hyperactive, yelling, mallet-wielding version was so pervasive and so fitted with what people think of Da Editor that one of the most common things said to him on being introduced in Real Life was "Hey, you're not short!"
Mr. Mind in the classic Captain Marvel arc "The Monster Society of Evil", commanded a number of Captain Marvel's greatest villains, including Dr. Sivana, Captain Nazi, Mr. Atom and Herkimer the Crocodile Man, shouting his commands via radio as no one would ever see his face. Turns out he was a telepathic alien worm, roughly 2-3 inches in length.
Vizzini from The Princess Bride, especially in comparison to Fezzik, one of his henchmen, who is a giant.
Rory Breaker in Lock, Stock & Two Smoking Barrels, the short but ruthless leader of the black London gangs. He's described as "that psychotic dwarf with an afro." His two massive bodyguards rarely have their heads in frame.
Forbidden Zone (the Richard Elfman movie) is ruled by King Fausto, played by Hervé Villechaize.
Cutler Beckett of Pirates of the Caribbean. While his height is never emphasized, he is notably shorter than every other character.
Arliss Loveless in the movie Wild Wild West, was a variation on this — he was an [considers phrasing carefully] average-sized person, but completely legless. Don'tsayit.... Both Dr. Loveless and Mr. Big were played by Micheal Dunn.
The Mule in Isaac Asimov's Foundation series. Played entirely seriously. He does however have psychic powers that he uses to control people.
A kind of strange version in Paezhar zo Myraq, better known as 'The Little Pigeon', is a slave owner and general in the Yunkish army. He is only five feet tall, and has his slaves specially bred for height, and wear stilts into battle, making them 7 feet plus. Most of the other regiments in Yunkai have similarly elaborate and impractical gimmicks, since the only fighting they've done for years is mock battles against each other.
Then there's Tyrion Lannister, a dwarf who's easily one of the most Bad Ass characters and effective leaders, though he has trouble actually getting put in a position where he can lead because everyone hates him, including his sister. When he is, though, Magnificent Bastardry results.
Eldest Gruff from The Dresden Files: Small Favor is the elder brother of a gruff approximately the size of an elephant, and makes ominous booming sounds when he walks. He's five foot nothing.
Variation in The Wheel of Time. Sammael is one of the most feared of the Forsaken, and the most visible villain for several books in the middle of the series. He's only slightly under average height, but unluckily for him, the people he hates and envies the most (rival Forsaken Ishamael and Demandred, his ancient enemy Lews Therin Telamon, and Lews Therin's reincarnation and current Chosen One Rand) are all very tall, and Sammael is extremely self-conscious about his height as a result, to the extent that Word of God has explicitly said he'd use magic to make himself taller if he knew how.
A feline example is Scourge from Warrior Cats. A tiny cat barely larger than a kitten, but also the leader of BloodClan and universally feared by all who know of him, and for good reason. No one is either brave or stupid enough to joke about his size, particularly since he uses it to great effect in combat, by slipping out of holds and generally being faster than his opponent.
Gus, the "Gucci dwarf" from Black Books, a feared London Gangster who's flanked at all times by two massive bodyguards and carries a fold-out highchair in a briefcase.
Mr. Big, the main villain from the pilot episode of Get Smart. As with For Your Height Only he's actually a midget, which is only revealed when Smart and Mr Big are in the same room.
Jasper Batt Jr. from No More Heroes 2: Desperate Struggle starts this way, but ends up growing bigger for the second phase of the fight. And for the third phase, he gets really big.
Salazar from Resident Evil 4. He fits the mold spectacularly, being a Napoleon-inspired short guy with two large bodyguards ( genetically engineered monsters, no less) flanking him. Oddly he breaks a tradition of sorts in video games by sending one after you at once and then fighting alongside the second (as opposed to watching on the sidelines and having both double team the player).
In MouseHunt for Facebook, the Nerg Chieftain Mouse is the smallest mouse in the tribe. It's also the most difficult one to catch in the Nerg Plains.
One of the villains in Borderlands 2's "Captain Scarlett and her Pirate Booty" DLC campaign is Sandman, a midget pirate captain. It's implied that he keeps order among his men via his vicious reputation, and the fear inspired by his massive enforcer the Big Sleep. Interestingly, nobody mentions his small stature except for he himself, and Scarlett is afraid of a one-on-one confrontation with him, describing him as being very strong.
At the end of level 28 in New Yankee in King Arthur's Court the "Dark Lord" was uncloaked only to reveal a midget on stilts. Destroying his fortress during it earns you the "Napoleon" achievement.
Galactamaru from Girl Chan In Paradise is portrayed with a extremely muscular build and a deep, booming voice, and is always shot via Hitler Cam...until the third episode, where he's finally put in the same shot as the heroes, revealing that he's less than a foot tall and easily defeated by Yusuke.
Lord Farquaad in Shrek. He's very sensitive about his frankly childlike stature, and tries to appear taller however he can. His palace is also the closest a medieval building could come to being a skyscraper. ("Do you think he's compensating for something?")
King Koo-Koo in Raggedy Ann & Andy: A Musical Adventure is about the size of a squirrel compared to the heroes, and is very, very touchy about it. His ultimate ambition is to be the largest king who ever lived, which he can only achieve by nonstop laughter. In the meantime, he makes up for his diminutive stature by reigning from a throne mounted on several elevated platforms high above his courtroom.
Clyde from the Ant Hill Mob in Wacky Races. Slightly subverted in that his henchmen are just as vertically challenged as him.
Many depictions of Napoleon Bonaparte portray him this way. Napoleon was actually around average height for a Frenchman of his time period, and would hardly be considered tiny nowadays, but soldiers tended to be larger and burlier than the average man for obvious reasons, causing him to look fairly undersized around his fellow soldiers. This effect was amplified by the fact that he was most often seen around the elite (i.e. larger and taller than average for soldiers) Imperial Guard. He was given the affectionate nickname "The Little Corporal" by his men. Britain, his sworn enemy, seized upon the perception and lampooned him in propaganda cartoons as a midget tyrant. Further confusing issues for the British, Napoleon was 5'3 tall in French measurements, but due to the fact that French feet were longer than Imperial feet this equated to 5'7 in British measurements.
In French, the word "petit" is usually interpreted to mean "little", but it can also mean modest or thin. The play-on-words was likely intentional among his soldiers (for endearing effect) as well as British propaganda (for slanderous effect).