Uncleanliness Is Next to Ungodliness

Appears mostly in works of fiction designed for children (and some for adults). But whenever the habits/daily life of the bad guys (either the Big Bad or his/her mooks) are shown, they tend to be absolutely disgusting, to the point where anyone living like that should contract several diseases, including leprosy and the plague, unless they die from food poisoning first. Usually these are Informed Attributes, but occasionally shown to make the bad guys really seem all the more disgusting (although sometimes they may come off as cool, especially if they're pandering to the preteen boy crowd.)

The trope showed up first (at least in the West) in Regency times, or about the time that the urban middle classes first had access to safe, clean running water. This is not a coincidence in the least. Before safe water was available, taking a bath really was more dangerous than remaining dirty. People who bathed were quite literally risking their lives to be clean - a sign of wicked vanity at the time. Compare that to women using Botox (a byproduct of a deadly bacterium, and one of the most lethal toxins on earth when uncontrolled) to remain "young"-looking today.

Compare with The Dung Ages, where everyone who wasn't a king lived like this (yes, even the lower rungs of the nobility). Contrast Creepy Cleanliness.

Comic Books

 * Done pretty realistically in Watchmen: Rorschach lives in absolute filth, with little or no concept of personal hygiene; it's noted by several characters that the guy stinks. It's not because he's evil, though - it's because he's really, seriously mentally ill and would rather maim criminals than take a bath (there are only so many hours in the day, you know).

Film (Animated)

 * Subverted in Shrek, who tends to have these disgusting habits, but is definitely a good guy.
 * Gaston in the Disney version of Beauty and the Beast was shown to have very stinky feet. Of course, wearing those big hunting boots will do that to even the cleanest of men, and Gaston probably enjoys the smell of his own sweat.
 * Froglet in the film of The Princess and the Goblin picks his nose in a truly grotesque manner, sprays it whenever he says it, and declares, with regard to the humans he's plotting against, "I WANT TO HAVE THEM EATING THE DIRT FROM UNDER MY FINGERNAAAAAAIIIILLLLSSS!"

Film (Live Action)

 * Jabba the Hutt. Enough said.
 * The title character of the David Cronenberg movie Spider has very poor personal hygiene.

Literature

 * Many of the villains in A Series of Unfortunate Events are like this. In The Penultimate Peril this is lampshaded when Kit tells the orphans that evil people can be recognized by unclean habits such as placing glasses of water on tables instead of coasters.
 * And not being well-read. However, it should be noted that there are villains in the books who are not unhygienic (such as Esme Squalor, who despite her name is impeccable to the point of obnoxiousness), and are very well-read, the latter of which makes them all the more formidable.
 * Profoundly averted in Discworld. Nobby Nobbs and Gaspode in particular are firmly on the side of the heroes but are revolting. Then again, Gaspode is a talking dog, and the dogs and werewolves of Discworld are terrified of baths. At at least one point there is a minor character who claims she is not one to think that cleanliness is next to godliness (and so following this trope) and the narration notes that, in fact, very few people do, not least reams of so called prophets etc, whose renunciation of mortal, ungodly matters often starts with soap.
 * Most of the vermin in Redwall; at one point Badredd is openly mocked by his comrades for having to bathe after getting trash dumped on his head because "he only took a bath last spring". It's not impossible that this is because the vermin of Mossflower tend to be slightly closer to their non-anthropomorphic counterparts in behaviour than the woodlanders.
 * Relg, an Ulgo zealot in The Belgariad is explicitly mentioned to be covered in dirt. He is also misogynistic, abrasive, believes himself to be favored above others by his god, obstructs the hero's journey with frequent prayer breaks, shuns physical contact and fears the open sky. Since he's one of the good guys, he eventually grows out of those things (finding his True Love helps) although the books never mention him taking up bathing.
 * Invoked in Diana Wynne Jones' The Magicians of Caprona, which features a long-lived feud between the Montana and Petrocchi families; the older children in each family tell their younger siblings stories about all the terrible, filthy habits of the other family, not a one of which is true.

Live Action Television

 * Ecoloco in the Mexican TV show Odisea Burbujas: He loves noise and smog; water and soap, he hates.
 * Monsters in Supernatural tend to have unclean lairs (the sewer lair of the season 1 shape-shifter, for example).
 * Averted in Buffy the Vampire Slayer with the Mayor, who is the Big Bad of season 3 and also the biggest Neat Freak of the series.
 * Criminal Minds: Sometimes this trope is played straight, sometimes averted (especially if the unsub suffers from obsessive-compulsive disorder.

Music

 * Murdoc of Gorillaz is notorious for this.

Newspaper Comics

 * Subverted in Peanuts by Pig Pen, who is continuously grimy to the point of being surrounded by a cloud of dust. At one point, Schultz reveals that this isn't because of poor grooming habits: he's just a dirt magnet. In one strip, he gets a make-over from Lucy, and over a sequence of panels, metamorphoses to his usual dirt-enclouded state just by standing there.
 * This happens another time when he exits the bathroom after a shower, and every particle of dust in the room flies towards him.

Tabletop Games

 * Dungeons & Dragons
 * Demon lord Juiblex is the demon who holds dominance over slimes, oozes, and puddings, and is himself a giant, sentient mound of sludge.
 * Evil giants are like this; the 2nd Edition Monster Manual claims that all their belongings are old, worn, dirty, and smelly, and in the case of fire giants, often burnt.
 * Ettins are worse. The same source says an ettin "never bathes if it can help it" and that searching their foul-smelling lairs can "be a disgusting, if not dangerous" endeavor.
 * Chaos God Nurgle from Warhammer Fantasy Battle and Warhammer 40,000. Oddly though, he is also the nicest Chaos God.

Video Games

 * Gruntilda from Banjo-Kazooie tends to have disgusting habits, according to her nice sister, Brentilda (such as bursting boils in her free time, or washing her hair in baked beans). Oddly, her cauldron says she's the second most beautiful character in the game. He might be brownnosing. But if he is, why would he bother bringing up Tooty at all?
 * In Okami, you get to explore the moon cave and help a chef mook with his appetizer for Orochi. The appetizer turns out to be called "Dungheap Goulash".
 * Not to mention that it includes 'wonderful' ingredients such as ogre liver.
 * The environments in the Silent Hill series get much of their evil vibe due to this trope. The rooms and halls are filthy and cluttered, the wall are grime-crusted, rusted metal everywhere, fire damage. This is most evident in the hospital scenes. Nothing living, sane or good can be expected to be encountered while walking through this environment.
 * At the same time, the developers note they wanted to give the environments a certain charm. While the areas are filthy and disgusting, it was also clearly, once, very pretty. This only serves to make it worse.
 * Also, pretty justified, in that the environments of Silent Hill are supernatural in origin.
 * The Mushroom Samba sequence in Mother 3 forces the protagonist to rummage through dustbins and bathe . Many of the mailboxes contain festering foods, or dead animals.
 * A rather Squick-inducing one in Luigi's Mansion 3: There are many places in the hotel where Luigi can use holes in the wall to peek into a room on the other side. In one of these, Luigi spots a ghost in a bathroom brushing its teeth... then scratching its behind with the toothbrush, and then continuing to brush its teeth. Ugh.

Western Animation
"Dr. Polaris: You gonna wash your hands? Flash in Lex: No... 'cause I'm evil!"
 * The villains of Biker Mice From Mars.
 * An episode of the Stargate spin-off Stargate Infinity has The Lancer catching the eye of one of the indigenous mud-creatures, who he finds absolutely repugnant. This becomes an Aesop at the end of the episode, where the mud-woman (as part of a grieving ritual or something) washes the mud off to reveal that she was a beautiful, blue-skinned humanoid.
 * In X-Men: Evolution, the Brotherhood lives in conditions that make the back alleys of third world countries look like palaces. The comicverse has the Nasty Boys, whose name says it all, though they make more sense when you consider the intended origin of their master/creator, Mr. Sinister: He was to have been an eight-year-old boy who was living an eight-year-old's idea of a really, really bad dude.
 * Averted in Beast Wars, where the heroes tend to be closer to their "animal natures" than the villains. Rattrap in particular is repeatedly pointed out as having an odor problem.
 * Also averted in Ed, Edd 'n' Eddy, Ed, a relatively well-meaning childish Ditz has notoriously horrific hygiene habits.
 * In an episode of Rocko's Modern Life, Rocko is berated by a genie for having spinach stuck between his teeth and shown a 1950's-era health-class film about hygiene and why it's important.
 * Hilariously parodied in Justice League Unlimited, where The Flash thinks this is the case when he's trapped in Lex Luthor's body.

Other

 * Orcs from various works are portrayed as gross.

Real Life

 * Robert Pattinson, star of the Twilight films. There are theories this may be an intentional attempt at scaring away the fangirls.
 * This stereotype of the Geek is unfortunately very prevalent. Your Mileage May Vary as to how much Truth in Television it actually is.