Black robes not fitting properly? Just try being a little more evil! Kicking puppies is good exercise after all! And don't worry about those meals you skip while you're scheming to take over the kingdom. Yes, the combination of your new villainous lifestyle and the laws of narrative causality will make those annoying extra pounds vanish before you can say "Are they even feedingYzma?"
Sometimes used for a Freud Was Right explanation, where the villain is nasty and vicious because she's so hungry. Very common among fashion-oriented shows to explain why the size 0 model is so cranky.
The reverse Villainous Glutton / Fat Bastard style is also relatively frequent (cf. Ursula, the Blob), but nowhere as lampshaded as the Lean and Mean look. Also contrast Large and in Charge. Particularly skinny or gangly-proportioned villains may qualify as Noodle People.
When the hero is stronger and/or dumber, this often leads to Brains: Evil; Brawn: Good.
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Anime and Manga
One Piece: Post-Time Skip, the three Admirals are all tall and thin. On a side note, Aokiji doesn't quite fit the "Mean" part of this trope unlike his fellow Admirals (namely Akainu).
Wapol is normally a Fat Bastard, but his Extreme Omnivore powers allow him to swallow his excess bulk and become sinisterly slender. He actually describes this form as "lean and mean" in both the 4kids and FUNimation dubs.
This also applies for Van Augur and Laffitte of the Blackbeard Pirates.
Orochimaru from Naruto is a fairly tall, lean man. Lean like a snake is more like it.
Envy from Fullmetal Alchemist, more so in the 2003 anime version. Incredibly slim and muscular with a form fitting body suit that really extenuates the slim physique. And "mean" rarely defines someone as it does him/her/it.
The demonic Violator from Spawn seesaws between this and Fat Bastard; as his alter-ego, Clown, he's an obese Depraved Dwarf with vaguely clown-paint like facial markings. As his true self, he's a spindly, emaciated, lanky-looking demon.
Most incarnations of Ragdoll in The DCU, but in The Batman it was taken to serious extremes; the Ragdoll is a tall, rail-thin thief and contortionist who is literally capable of fitting inside a top hat. Also, as he is often depicted as frail.
Loki is probably the skinniest male in Asgard. He is also one of Thor's meanest villains. Mind you, it only holds when compared to Asgardians. When compared to most normal humans, he seems pretty toned.
Invoked by Big Eater Volstagg in Journey into Mystery, who explains his distrust of kid Loki by saying that, like his previous incarnation, he picks at his food.
Rake of the Bounty Hunters in Gen 13. 6'5", 135 lbs, he's called Rake because of the long, metal claws on his hands. He's also a sadistic killer who likes to carve people like pumpkins.
Judge Dredd: The mass-murdering Judge Death is a very skinny fellow, mostly because he's an undead spirit inhabiting a corpse. He's quite tall but only weighs around 67 kg. He's also surprisingly strong for his size, being able to throw boulders into the air with ease and lift people up as if they were nothing.
Yzma of The Emperor's New Groove takes this to a new extreme, although it's not unreasonable to assume she may have been most attractive a century or two ago. She was shown to be quite attractive as a teenager in the episode "Cool Summer" of the show.
Scar of The Lion King is much skinnier than Mufasa and Simba or even some of the lionesses. He even points out his lack of brawn earlier in the movie.
And then there's Dr. Facilier from the new The Princess and the Frog. He's thin to the point of stylized in an otherwise rounded, naturalistic-proportioned world. He also shows off his belly-button with a midriff-bearing shirt.
Metropolis: Joh. Fredersen, ruler of Metropolis, has an assistant only credited as "The Thin Man". And while most of his scenes got chopped out in subsequent releases, it's indicated in the 2002 restoration that he beat the crap out of Josaphat trying to find out what Freder was up to. (This may need to be edited once the full restoration with the missing scenes comes out.)
Home Alone: Inverted in the first two movies, where short, round Harry is clearly the more malevolent half of the Wet Bandit Gang. Tall, skinny Marv, by contrast, borders on Ineffectual Sympathetic Villain much of the time.
In Harry Potter, Voldemort is often described as being tall and thin, with long, thin fingers. Snape is often described as thin, perhaps to invoke this trope, even though he is not evil per se. It's more implicit in the first five books, but definitely true of Draco Malfoy in Book 6 when he starts to visibly lose weight as a result of the stress of his assassination mission.
Several characters in Discworld have this aesthetic, even if they're not necessarily evil:
Lord Vetinari is a scheming Machiavellian dictator and is thin as a rail, voluntarily subsisting on nothing but bread and water. However, while he describes himself as evil, he is never an outright antagonist and is often on the heroes' side. Strangely, his (unnamed) appearance in the first book is as a Fat Bastard, and was generally considered to be his predecessor until Word of God confirmed they were the same character.
Granny Weatherwax, a manipulative Good Is Not Nice character in the same vein, is also tall, thin and wears black, though her slimness is not quite emphasized as much. It's more obvious contrasted with her fellow witch and lifelong friend, the short, plump, amicable Nanny Ogg.
Lacrimosa in Carpe Jugulum, who actually is evil, is the epitome of this, though, especially lampshaded in that she's mostly seen from the POV of Agnes Nitt, a large girl of roughly her own age...
Utilized, and oft-lampshaded, in Robert Jordan's The Wheel of Time novels, in that all skinny innkeepers that the protagonists come across in their journeys are invariably up to no good.
Timeline-191: Jake Featherston, the Hitler-esque Southern dictator of Harry Turtledove alternate history series, is described as whipcord-lean.
In Peter David's book Knight Life, Morgan le Fay has grown obese without the presence of Arthur or Merlin. But when Arthur suddenly appears in present day and decides to run for Mayor of New York, she not only becomes evil, but thin again.
Professor James Moriarty from Sherlock Holmes is described as being very tall and thin and like a lizard. This is probably to make him an Evil Counterpart of Holmes, who is himself very tall and thin.
A Song of Ice and Fire: Vargo "the Crippler" Hoat, leader of the murderous Bloody Mummers, is described as a tall scarecrow of a man. Bronn, the badass sellsword, is said to have a lean, wolfish look to him.
In his appearance in Galaxy of Fear, the Dark Jedi Jerec is described as being painfully gaunt and on the verge of emaciation. In his later appearances, like the Dark Forces Saga, he's got more weight and muscle, perhaps because he knew he'd have to rely on the Force less and fight more, and bulked up.
David Bowie's late seventies persona, The Thin White Duke, although not being evil, per se was definitely a bit sharper edged than his other characters and more than a bit coke-fueled, therefore somewhat delusional. This incarnation of Bowie has been described as "an amoral zombie", "an emotionless Aryan superman", "a mad aristocrat" and by the man himself, "a nasty character indeed". As far as the lean side goes, his weight plummeted to less than ninety pounds, extremely underweight for a 5'10" frame.
Many punk rockers in the 1970s were regarded as this by the establishment.
Warhammer's Dark Elves fit the trope very well, being a people composed entirely of vicious heartless sadists and having the slender, lean physique common to all elves. The leanness doesn't cause the meanness here, however, as their High and Wood Elf cousins are just as thin.
The Mourngul monster (from Monstrous Arcanum) is a causal version, however. It's a giant-mouthed ever-hungry ghost creature with a stick-thin frame and a ragged tear curtailing it at the waist. Mournguls died an agonizing death from hunger (usually after a stretch of starvation-induced cannibalism) in the frozen wastes, and their dark, all-consuming but futile hunger is all that is left of them.
The third edition of Dungeons & Dragons gave this option to characters with the Willing Deformity feats Tall and Gaunt. In this case, the Mean comes from the prerequisite of an Evil alignment, the assumption that people willing to fast themselves to half their natural weight or stretch themselves out on the rack probably have a few screws loose, and mostly the fact that the feats were introduced in the Book of Vile Darkness sourcebook.
The Spy from Team Fortress 2 is incredibly impolite (the Spy has banged the Scout's mom and loves to boast and troll the Scout about it, which could make you feel sorry for the biggest Jerk Ass in the game that Scout undeniably is) and very tall and slender, which his badass-in-a-nice-suit attire makes even more noticable. Furthermore, also alongside Scout and Sniper, he's the most prone to calling the Heavy "fatty" and "morbidly obese".
The Administrator, when she appears in the supplemental materials, is very thin, and seems to be totally amoral and have no emotions other than anger.
Both Mitsuhide and Mitsunari from Sengoku Basara are Ax-CrazyWhite Hair Black Hearts who are also tall and almost skeletal in appearance. In Mitsunari's case it's because he's too busy angsting to eat, while Mitsuhide is probably just that evil.
Battle Realms: The entire faction of the Lotus clan. Everyone is tall, skinny, and gangly, this is because of the paths their clan follow, in which they have to endure painful rituals which cause their bodies to rot in order to master death.