Jason Beck from The Big O. When he's not being an egotistical fop, he's actually frighteningly competent. Too bad this is overshadowed by his over the top hubris, which pushes him firmly into the "Laughably" part of this trope.
Most of the villains of early Dragon Ball are like this. Such villains include General Blue, who is utterly hilarious in personality (and also Camp Gay) but also a very deadly opponent, and Emperor Pilaf, who has no idea what he's doing. Also Majin Buu, especially in his Fat Buu form, where his antics and are so childish, goofy, and cartoonish that you almost forget that his "games" are killing millions of people, at least until the Establishing Shot of the barren wasteland where a thriving city used to be.
The Team Rocket trio from Pokémon are this, which is the reason why they are so popular. At least until Best Wishes, when their boss gives them an actual serious assignment.
On the opposite side of the power spectrum is Kaku. The second most powerful member of Cipher Pol 9, he can transform into a giraffe. No, you didn't misread that. He can transform into an actual giraffe. Even better, he can transform into a half-man/half-giraffe. One that keeps his trademark square nose. He sincerely believes giraffes to be powerful creatures and during his fight with Zoro was prone to defending them by saying such things as "Witness the power of a giraffe!". Though that could be part-denial since everyone keeps mocking him for his powers. Oh, and he uses his nose as a weapon.
Believe it or not, out of all the animals characters can transform into so far, the giraffe appears to be one of the very best (in this form his storm kick attack was amplified like crazy, he can shorten his neck to lengthen his arms and legs, he can shoot out his head like a cannonball ...). The only one that seems to be superior is the rare phoenix.
Any animal that can kick a full-grown lion ass-over-appetite is powerful, even if their goofy build and lack of vocalizations in the range of human hearing obscures that fact.
What makes the fight even funnier is that Kaku has just eaten his Devil Fruit, and is figuring its powers out as he goes along (bear in mind that many Devil Fruit users have to spend years learning their powers; for example, flashbacks show that when Luffy ate the Gum Gum Fruit, he had to go through quite a bit of training before he could even throw a proper punch). Crowning Moment of Funny comes when he discovers the aforementioned "shorten neck to extend arms and legs" move, reasons that it works on the same principle as a pasta machine, then names the move "Pasta Machine." Also in his favor is that, despite being a government agent, he's a pretty chill guy, even giving a good-natured laugh to a post-battle quip from one of the heroes.
Mara from Ah! My Goddess. She takes time out of her busy day tormenting goddesses and attempting world conquest in order to knock a child's ice cream cone out of his hands to fulfill a snide wish by his sister. Either Kick the Dog, Crowning Moment of Awesome, or both. A truly admirable commitment to evil on any scale. For those who are wondering this happens in the first season of the TV series — if not in Mara's first episode, then in her first or second appearance after that. The scene in question actually makes her seem oddly like a Disgaea character, laughing maniacally at her "evil deed" and resulting in both of the kids kicking her in the shin simultaneously and high-tailing it, to her angry surprise.
Baki and Minki from Hell Teacher Nube. They're (nominally) evil, powerful, hugely destructive Oni, but the former adores ice cream, toys, and riding around on the little kids' train in the park, and the latter has some bizarre notions of what a good big brother/little sister relationship should be like.
Gates of Full Metal Panic: The Second Raid is so over-the-top with his Chaotic Evil antics that everything he does is completely random. Despite the sadistic violence, this makes him even funnier.
The various teens of Ranma ˝ could conceivably come off as this, as opposed to Comedic Sociopathy. Not one of them (except for Kasumi, and even she made mischief on some occasions in the early manga) has done something that doesn't make them look at least partially villainous, yet these same deeds (and the regulars who generally are villains) still manage to be funny because of their attempts at evil.
Almost all of the Order of the Glittering Star from Star Driver. Their everyday personas are so over the top that you can't fully take their villain sides seriously - all of them being hammy certainly helps too.
Blastmon from Digimon Xros Wars is said to be immensely powerful, but has the mind of a 5-year-old and calls the other generals by nicknames. Then he's defeated by the heroes and is reduced to a hopping head for the rest of the series. Before him, there was Etemon, an over the top rockstar monkey who's both silly, and far stronger then the last Big Bad.
The aforementioned Batch and Gluko are also quite comedic. Quite often at the end of many episodes, Gluko often happily stands by and adores the scenery while Batch and Eccentro get rather embarrassing moments. They even get into rather comedic situations involving Ms. Loon.
Laharl in Makai Senki Disgaea has quite the reputation for having some rather funny moments. Also, in Episode 3, Vulcanus becomes this when he accidentally almost falls off a statue and causes it to fall, which leads to Flonne and Etna's clothing & personality swaps. When he finds Flonne sleeping with Laharl and Etna, he flips out and hits her with a This Is Unforgivable and attempts to kill all three but accidentally falls into a clam exhibit and is unable to get out for the rest of the episode. Later, while he's still trying to get out, he knocks over the same statue again, causing clothing swaps again, this time for Laharl, Etna, Flonne, and one of the Prinnies.
Before he went all One-Winged Angel, Father had a tendency to make small, sardonic quips while horrendous battle raged all around him - usually along the lines of "Why does everybody feel the need to demolish my home?"
In a similar case to Barry, Ladd Russo from Baccano is a complete nutjob who loves killing just for the sake of killing. While it can be argued whether or not his actions are intentionallyPlayed for Laughs, it's hard not to enjoy watching the guy have so much fun.
Macine Baron from Steam Detectives. A bumbling collector and inventor of steam-powered robots with a hilariously overblown Austrian accent; willing to steal the robots if he feels like it. Certain robots he's got his eye on are more-or-less Steampunk Roombas. Upon being defeated by Goriki, he develops a deep affection towards "him".
Jan Valentine of the Valentine Brothers assassination team from Hellsing, he's very sadistic and cruel and he's also hilarious, he's very foulmouthed and loves to tell disgusting stories, he also treats the assignment like a game, and in the manga long after he's been killed he shows up from time to time to break the fourth wall.
The Joker thrives on this trope. One of the main goals towards portraying the character is to make his actions such that you can laugh one moment, and be horrified the next. Brilliantly brought out by many of the actors to portray him in other media, most prominently Jack Nicholson, Mark Hamill, Heath Ledger and, most recently, Brent Spiner. Whether it's electrocuting a gangster while singing showtunes, casually (and cheerfully) stalking an everyday accountant in the middle of rush-hour traffic, or doing a magic trick by making a pencil disappear, you can always find it either way with the Joker. Cesar Romero too. Maybe it's because he was so harmless or such a Large Ham, or maybe just because the show was So Bad, It's Good, but he was genuinely hilarious, if not nearly as terrifying as Ledger's Joker.
Paul Dini on the Joker: Joker's that perfect combination of schoolyard bully and class clown. The kind of sicko who will make you laugh just before he sticks the knife in and twists it.
Part of what makes the Joker so terrifying is his special mixture of being funny as all get out but a Complete Monster in many a canon. While other villains have managed to pull off this combination, the Joker is probably one of the best examples in fiction.
Herr Starr from Preacher. Every time he shows up he has a smartass line, but his Crowning Moment of Funny was when he scares some poor old lady for blocking the moving walkway by shooting wildly at her.
By this point in the series he's had to deal with "an angel, a whore, an eunuch, several dozen idiots, an unkillable mick, a one-man holocaust in a duster coat, the occasional twenty-course banquet for the mother of all fat fuckers, inbreeding, family feuds, bulimia, a retarded child (always good for a laugh), and the utter destruction of our most sacred shrine and secret retreat in the detonation of a fifty-ton bomb." Not to mention "having my head carved into a giant gleaming dong", so it's understandable that he'd be a mite testy.
Yzma is so over the top in her characterization and frequent lampshading of standard Disney villain tropes that she's somewhere between this trope played straight and a parody of it. It also doesn't hurt that the character is voiced by Eartha Kitt.
In The Incredibles, Syndrome is another Disney villain who is both humorous and unnerving. Many of his lines will sound very familiar to anyone who is a comicbook fanboy or knows one, and his goofy, hammy demeanour can almost make you forget that the guy is guilty of mass murder, would knowingly kill children, and is essentially plotting to start killing hundreds of innocent people and get hero-worshipped for stopping. Just as an example:
Elastigirl? You married Elastigirl? (notices the children) And got bizzaaaay!
Hades from Disney's Hercules. Thanks to James Woods, he changed from being a stereotypical chilling villain to fast-talking, tempestuous and absolutely awesome. Easily the best part of the movie.
Adenoid Hynkel from Charlie Chaplin's The Great Dictator. He is portrayed as infantile and crazy from power. Some consider this version of reality to be too humorous.
Ray "Bones" Barboni in Get Shorty. He can spin on a dime between being menacingly brutal, intentionally funny, and humorously incompetent. In one scene, he beats a character half to death and almost gets his balls blown off in the process. When Dennis Farina plays villains, they are usually both funny and nasty at the same time.
Tuco in The Good, the Bad and the Ugly - it's debatable whether he's actually evil, because some consider him the most sympathetic and relatable character in the film, but he's far from a good guy and is absolutely hilarious.
The villain of the CarrotTop comedy Chairman of the Board is the only particularly funny thing about it. It isn't worth it.
The Ciaphas Cain series tends to draw from this trope for its humor, only instead of the source being an individual villain, it is the Darker and Edgier nature of the Warhammer40000 setting itself that provides the source.
The pigs from Animal Farm can be this, especially Squealer. A case in point would be the morning after the pigs get wasted on booze and it is mawkishly announced that Napoleon (now suffering a hangover) is dying. Then: Great news! Our dear leader is going to be making a complete recovery. Anyway, I'm off to procure some books on brewing. Oink!
All of the villains in the Adam WestBatman show fit, but the best examples are all of the one-shot villains that are unique to the show. And the Riddler, whose infamous riddles would continuously be solved by a Boy Wonder who was otherwise only good for getting kidnapped.
Spike could be quite funny, such as when he passed out in Angel's backyard and woke up when the sun made his hand catch fire. Also in the episode where he watches from a roof-top while Angel saves a girl and provides sarcastic voice-over narration.
As Victim: Oh, how can I thank you, you mysterious black-clad hunk of a night thing? As Angel: No need, little lady, your tears of gratitude are enough for me. You see I was once a badass vampire, but love, and a pesky curse defanged me, and now I'm just a biiiiiig, fluffy puppy with bad teeth. As Victim: But there must be some way I can... show my appreciation. As Angel: No! Helping those in need's my job, and working up a load of sexual tension and prancing away like a magnificent poof is truly thanks enough. As Victim: I understand. I have a nephew who's gay, so- As Angel: Say no more. Evil's still afoot. And I'm almost out of that nancy-boy hair-gel I like so much. Quickly, to the Angel-mobile! Away!
Angelus is even funny sometimes, in a sick sort of way. ("Othello and Desdemona! My favorite couple. Only Desdemona didn't love the other guy.")
The Trio start out as a mix between this and Harmless Villain. Then one of the subjects of their wacky hijinks points out that their Black Comedy Rape plan wasn't quite as funny or as hot to her, retroactively pointing out the Moral Event Horizon was crossed much earlier in the ostensibly funny episode. The Trio reacts differently: Warren goes monster, Andrew becomes an Ineffectual Sympathetic Villain, and Jonathan tries desperately to do a Heel Face Turn but is prevented by the other two.
Chris Jericho was one of these in WCW and in his early days in WWE. When he returned to the WWE, he tried to be a face, but has since lapsed back into this, and is much better.
Santino as a heel is this, typically throwing silly insults at his opponents. Usually he's a weak character who gets whipped on, to get the audience cheering for a big face.
Da Orkz of Warhammer 40000 are a race of Psychopathic Manchildren who fill in as the comic relief of the setting, in no small part due to crossing the line twice. Most factions in Warhammer 40k will wage genocidal war on you because they hate you with the burning fire of a thousand suns. The Orks will wage genocidal war on you because it's their idea of entertainment.
Since 40K is in many ways WarhammerIN SPACE!, the Orcs and Ogres in Warhammer Fantasy have similar traits.
In Nomine features Kobal, the Demon Prince of Dark Humor. There is also his "blood brother" Haagenti, the Demon Prince of Gluttony, who also holds purview over torture and sight gags (which many consider to be a form of torture).
Pathfinder goblins, bless their psychopathic little hearts.
Goblins in any given Magic: The Gathering setting tend to be psychopathic, destructive, homicidal, genocidal, suicidal and absolutely hilarious.
Edwin from Baldur's Gate and its sequel is sociopathic, irritable and has a massive ego but is genuinely cranky to the point of amusement and bumbling enough to be this trope. Half the laughter comes from him being sulky.
Many, if not all, of the main enemies in the Super Mario Bros series. From Bowser's kidnapping of the princess turning out to be lovesickness, Wart being the tyrant of a dream world while critically weak to vegetables (he hates the taste), to even the names of many of the stage bosses (King Caliente's Spicy Return!). Not to mention anyone who's an antagonist in an RPG or spinoff (*Chunks Awaaaay!* ) (I HAVE FURY!).
Special mention also goes to Dimentio, who often has rather quirky behaviors that count as somewhat comical, and yet commits genuinely horrific actions while cracking jokes.
Escherion, the very first Lord of Chaos in Adventure Quest Worlds, becomes this trope at the end of the Chiral Valley saga when the hero reflects his inversion spell right back at him, inverting him and causing him to suffer the Humiliation Conga of ending up casting every spell he tries to cast on him/her on himself, and eventually turn himself into a harmless frog, which is a rather funny scene, to say the least.
Hero: (after Escherion turns into a frog) Huh... I guess you inverted your powers. Every spell you try to cast on me, you actually cast on yourself. Escherion: *ribbit ribbit* Hero: I'm sure you just said something very rude in froggy.
The Lich Palawa Joko in Guild Wars: Nightfall once terrorised the entirety of the continent of Elona, whose forces were the greatest threat said continent faced until the Charr invasion many centuries later. Being unable to die or be killed, he had to be sealed away at the location of his defeat, and there he would have remained... if the plot hadn't required that you release him from his imprisonment for several very good reasons. But that's okay, all Joko wants is to reform his undead Army Of Darkness, which you've got to help him with as well. Astoundingly, he fails to be a threat for the remainder of the game, and while you're dealing with the Big Bad he's spending the rest of the time hilariously failing to get any sort of organisation from his mindless minions. What a guy. By the second game, he has gotten his act together, and how.
Mad King Thorn is generally loved by players and seen as wacky and amusing. The fact that he and his minions will happily recall the horrors they inflicted on their subjects, such as once having an entire village flayed alive, makes this somewhat inexcusable.
Naturally Dr "Eggman" Robotnik of the Sonic the Hedgehog series, and only seems to be leaning further this way as of recently. Many alternate media representations are similar (see below). What do you expect from an egg shaped scientist who makes toy-like robots?
Grand Theft Auto San Andreas. James Woods as Toreno, the paranoid government agent. Disrespecting dead women to a monologue on how all modern conspiracy theories are nowhere near the truth.
General Sarrano is an evil, manipulative, foul-mouthed bastard who delights in the suffering of others, gleefully betrays everyone around him, and is generally an all-around un-fun guy to be around. At the same time, he's a hilariously over-the-top jackass with a never-ending stream of creative invective to toss at anyone and everyone around him.
Handsome Jack in Borderlands 2. He is evil. Absolutely, totally evil. And he is such an epic asshole that every conversation with him is side-splittingly hilarious.
Essentially all the villains in Sluggy Freelance except, arguably, Daedalus. Horribus, in particular, is a big example. One moment he's begging for his teddy bear (making him vice president to his empire, no less) and getting hit in the head with anvils in the middle of his Dramatic Entrance, the next he's incinerating minions and dropping a bridge on the heroine.
Darksoul in the oft-underappreciated "Oceans Unmoving" storyline is a borderline example, whose humor mostly comes after you find out the plot twist; He is actually the present day Bun Bun, while the Bun Bun shown is from the past; present day Bun Bun (Darksoul) has Laser Guided Amnesia, and his pseudo-deadpan snarking is actually him ticked off on the fact that he has no idea what's going on; everything his past self is involved in is ridiculously random ("Leaf people?"), and he knows he should know what's going on.
Even Daedalus can be funny. The only villains who weren't affably evil were Evil Aylee Clone and Kusari, who usually plays the straight man to the laughable evil around her, and even when dressed up as 'Hello Kitty' was more chilling than chuckle-worthy.
Bizarro is a creature with all the powers of the Man of Steel, and an intellect that insults egg plants by association. To be fair, he may actually be quite competent, especially in the DCAU where he is the only one to notice that something is wrong with Lex Luthor (namely that Lex and Flash are body swapped), but because he expresses himself in opposite action every time he speaks, no one gives him the time of day.
In Transformers Animated, Blitzwing by himself is funny, particularly when his "random" personality is in control ("Ooh, I wanna see him turn into a fire truck, can I, can I, can I?"), but him and Lugnut sniping at each other is hilarious.
Extra points for being a pretty competent and evil villain - one notable appearance includes tearing off Ratchet'shand (and making a reference to eating it some episodes later. Hilariously.).
Other villains have their moments, too, some more than others. Swindle, for example, is an Arms Dealer who acts like nothing so much as an overly-excited infomercial host. (In fact, his mannerisms were based partly on Ron Popeil.) And, because this show is so Merchandise Driven, you can have your own little plastic Swindle for just $10.99! But Wait, There's More!!
Dave The Barbarian's Dark Lord Chuckles, The Silly Piggy. It's in the name. For bonus points, this is how he actually announces himself.
Aku from Samurai Jack is so much fun to watch that you often forget he's Made of Evil, as he takes a break from hunting Jack to villainously order a pizza, subjects frightened children to his terrible storytelling, and swears revenge in a helium voice while in the form of a kangaroo rat.
The "storytelling" thing may have been an attempt to raise the next generation to revere him. It fails, obviously.
Skeletor from He Man And The Masters Of The Universe became this in the Filmation cartoon —in the original minicomics he was a fairly serious villain, but since censors were constantly breathing down Filmation's neck about what they perceived to be a horribly violent cartoon about a sword-swinging barbarian, they decided to make the scary man with a Skull for a Head less scary by playing him for laughs. Though still an evil schemer, the cartoon Skeletor was turned into a Laughing MadDeadpan Snarker who kept cracking one-liners in which he insulted the world in general and lamented how he was Surrounded by Idiots. The 2002 remake of the show turned him a little more menacing and threatening, but kept his sarcasms and general tendency to get all the best lines in the show.