David Xanatos from Gargoyles is usually one step ahead of the Gargoyles, and everyone else. He frequently got away with actions that would send a normal man to jail for the rest of his life (although he was jailed for a short time), and was a member of the Illuminati's guild. Since Xanatos was such a smooth talker, he would make you believe he was your friend all while positioning the knife in your back.
Xanatos's creation, Thailog, is one as well, solidified when he betrays and then outwits his maker in his very first appearance, leading a fearful Xanatos to speculate that Thailog may be even smarter than he is. Going by the comic continuation, Thailog seems to have inherited his father's fondness for schemes that profit him no matter the outcome as well.
Let's not forget Xanatos' wife, Fox, who also managed to outsmart him on one occasion. He even refers to her as his equal! His proposal to her amounted to "We get along, we'll have good kids, and we're the only ones as smart as each other."
Megatron of Beast Wars: He's a user and abuser of his followers, a gloating sadist who enumerates the ways he's beaten his enemies as he's standing over them in his moment of triumph, a master manipulator who is only served by his underlings' treachery (to the point of keeping two victims of Chronic Backstabbing Disorder around just to keep himself sharp)... and yet he carries off scheme after scheme with audacity, panache, and an almost vaudevillian flair. Nor does he work in small potatoes; his schemes include two bids to rewrite history as well as consuming his namesake's spark to add to his own personal power. In the sequel, he manages to become a God. Magnificent. Bastard. Yesss.
His Transformers Animated counterpart also comes close, if not equal with him. This guy manipulates Sumdac to repair his body, avoids the mistake of his predecessors by killing Starscream the first chance he gets, coaxed the Constructicons into his employs with just a couple barrels of fine oil, and he Out-Gambitted Starscream to ensure that the Omega Supreme clones didn't imprint on Starscream or Megatron himself, but on the loyal Lugnut. And when he got physical, he got physical. In a rather defining moment that puts him in this trope, after receiving the Allspark Key which grants him a new body, he subsequently pummels Optimus Prime and the rest of the Autobots. When Optimus effectively tells him to bring it on because he won't give up the location of the Allspark, Megatron reveals he already has the Key which will lead him directly to it and that he was only kicking the crap out of Optimus for his own amusement.
Impostor Dan, from Dan Vs. After stealing Dan's identity, and endearing himself to everyone in town, he is finally taken down by Dan. Being a Magnificent Bastard, he gets out of prison and becomes a telemarketer. He uses his position to drive Dan insane, using a hidden transmitter to act as the voice inside his head, renting an apartment, just to capture them both, and knowing the characters so well that he can place traps exactly where they will be. When Dan chases him with a baseball bat, he gets a cop to taser him twice. He even manages to do all this while being completely likable, suave, and normal.
Dolf from Alfred J. Kwak. While he may start off as a mere naughty kid and a bit of a bully, as the series progresses Dolf becomes more and more devious and evil, to the point where he becomes an Adolf Hitler Expy. After years of being abroad, Dolf returns to Great Waterland and manages to stage a coup d'etat, removing the King from his palace and even amassing an army. After falling from power, he returns again after the King has abdicated and now partakes in the first democratic election. In order to get ahead of the other candidates, he hires foreigners to damage the dam that keeps the land from being flooded. He then drops out of the race, saying he has to help the people and can't waste time on elections. He then publicly funds repairs of the dam, making him immensely popular and boosting his chances at the election once he reenters. The only witness, a jellyfish spy called Lispel, attempts to blackmail him, which promptly backfires when Dolf attempts to shoot him to death in order to eliminate any chance of his plans being foiled. Had Lispel not survived the shooting and informed Alfred, Dolf's plan would have succeeded.
Megabyte from ReBoot. The low, British baritone voice of Tony Jay certainly helps, but this is one of the few cartoon villains that has never suffered from any sort of Villain Decay, and is actually considered more dangerous as the series progresses. His most magnificent moment (besides the guitar duel) is when he took advantage of the web invasion and subsequent Enemy Mine situation to strand Bob, Mainframe's champion, in the web. While Daemon is more powerful and dangerous, Megabyte's return in season 4 evoked much more fear from the main cast. What makes this so Magnificent is how his dispatching of Bob is so un-magnificent. He shoves him and presses a button. Dead easy. It also helps that judging by the season four cliffhanger, he wins.
Princess Azula from Avatar: The Last Airbender. She's a sociopathic firebending prodigy, but she does it with such style and planning that you can't help but admire her (but hopefully not too much). She manipulates everyone around her, including her own brother, and her plans in the second season require her to out-maneuver another Chessmaster, Long Feng, which she does, effortlessly. Her Crowning Moment of Awesome was conquering Ba Sing Se, and by extension the whole Earth Kingdom, by taking advantage of the political instability with only her wits and two (non-Bender) friends and, in the process, nearly killing Aang with a lightning blast in the middle of his Transformation Sequence in the second season finale. She's only 14.
Azula is succeeded by Amon in The Legend of Korra, who has obtained this status in record time, SIX EPISODES! Every thing this guy does only gains him more followers. He sends a threat to city hall, and knows that they won't listen and just heighten security at the Pro Bending arena. He then has his fellow equalists disguise as simple audience members and sneak in their weapons by hiding them in their popcorn. Turns out he wanted the entire police force there so he could take them all out at once before they could stop him and show the whole stadium how powerless they were. He also might have paid off the Pro Bending referees to not call out the Wolfbats team's cheating to ensure that they'd win the match, so Amon could then make an example of them by taking away their bending. And he knows how to take advantage of the situations: he always makes sure that people see the truth of his extremist beliefs that benders abuse their powers. It helps that the first thing we ever see him really do in the show is taking bending powers away from dangerous crime bosses.
Korra Book Two brings us Varrick, the goofy, charismatic Uncle Pennybags of an executive who befriends our heroes in the first few episodes before talking them into helping him escalate a regional conflict into a full-scale war, smuggle in weapons, organise a small military coup, and buy up everything they own whilst still keeping them completely convinced that he's on their side. As he cheerfully puts it, "If you can't make money during a war, then you just plain can't make money!" By the time anyone finally realizes he's only out for himself, he's already succeeded in stealing all of Asami's remaining goods then convinced her he's "saved" her company by buying it out. He then gets the only person who suspects him thrown in jail, and, if Bolin hadn't happened to spot the boat left by his soldiers, he likely would've succeeded in kidnapping President Raiko and convincing Republic City to send troops to the war front, earning him even more money. Even when he's jailed, he's not phased by it, since his company made the prison and he designed himself a Luxury Prison Suite in the likely event he ended up in there. He then lends the Krew his personal battleship as an act of goodwill. He ends the season escaping justice by taking advantage of the chaos Vaatu is causing and using a hang-glider which he just happened to have smuggled into his jail cell in the event an aerial escape opportunity presented itself. When he's next seen in Book 3, it's in Zaofu, being treated as a guest of honor and going completely unpunished for any of his actions. Su Yin trusts him and believes he deserves another chance. Throughout the show Varrick manages to be surprisingly ingenious in his plots, Crazy-Prepared for any eventuality, and genuinely affable to the Krew even as he's manipulating them or screwing them over for his own interests.
As of Book 4 we can now add its Big Bad Kuvira to the list. Like Amon, Kuvira is a Villain with Good Publicity who has so far managed to outmaneuver anyone who's challenged her. She even breaks Amon's record and earns her status in one episode! In "The Battle of Zaofu" she anticipated that Suyin would try to attack her and set up a clever Batman Gambit to capture them making it look like they were the aggressors while maintaining her Villain with Good Publicity status. That forced Korra to challenge her to a one-on-one duel for Zaofu, which Kuvira wins (though granted, the fight was full of Idiot Ball moments on Kuvira's part and she only won due to something she couldn't have planned on). She then attempts to kill Korra, which works out either way because it would either eliminate the Avatar or force Jinora and Opal to violate the duel. The latter gives her just the excuse she needs to invade Zaofu. And though Bolin and Varrick managed to escape, Bataar Jr. has seen enough of the spirit vine experiment to restart the project with Zhu Li's help. In other words, she won decisively. And then there's "Kuvira's Gambit" Kuvira knows that Republic City has been warned of her coming attack, so she moves up the schedule to one week instead of two. In addition, they believe that she is transporting the cannon by rail, so they attempt to disable rail transport; anticipating this, she deploys the cannon on a Colossus instead. And when presented with a Sadistic Choice of leaving Republic City or never seeing Bataar Jr again, her response is to (Though not without a great deal of regret) Shoot the Hostage.
Nerissa from W.I.T.C.H. is hands down the second best manipulator in the television series. Her schemes have spanned over ten years to complete her goal of universal conquest to unite all words, Nerissa takes on multiple false identities to help defeat Meridian's evil ruler Phobos by posing as a castle servant to pass information to the rebel army.
Why the second best? Because Will, her counterpart in the current generation of Guardians, ultimately tries this... And proves herself better, effortlessly putting her in an inescapable situation by using Phobos and, when he obviously uses the power he acquired in the process, manipulating him into losing it. She's 15.
Aladdin: The Series has Mozenrath, comparable to Jafar from the Aladdin movies. (See also the film example section.) Even though the confidence was always there, Mozenrath was able to back up his smugness from the get-go. His very first plan involved using Genie as bait for a magic-devouring monster, in order to make Aladdin capture it for him, thus setting up a simple but yet effective Xanatos Gambit. While it didn't last for long, Mozenrath did indeed end up with the beast under his control. Aladdin and his friends did face many capable enemies during their adventures, but Mozenrath was the one who really made them sweat, always pulling something from his sleeve to put the odds back in his favor. If that wasn't enough, the lad was also blessed with a silver tongue that really got our heroes on the nerves. Really, he spends one episode just sitting on his throne, snarking and gloating to a locked up Aladdin, and it still didn't end in a complete loss for him. After all, there's a reason why he's the only villain to ever hear Aladdin say the words "You win".
Dogbert on the series Dilbert whose "religious belief" is "that everyone exists for the sole purpose of entertaining me." On one episode, he sets up a carnival booth where you "knock a street urchin off a beam with a baseball and win a toy." In another, he convinces Congress to abandon all holidays in favor of National Dogbert Day (The traditional Dogbert Day feast: the bald eagle. He wanted something special) for the sole purpose of being annoying. (The same reason he invented Secretary's Day.)
Tombstone in The Spectacular Spider-Man proved himself to be this upon his very first encounter with Spider Man. He floors the webhead in one swift move, antagonizes him by telling him how he is fighting a losing battle, uses it as an attempt to get Spider Man to do what he wants and finally makes Spider Man look bad in the eyes of the cops. All in around five minutes.
Dr. Octopus as "The Master Planner" has also obtained this status. He operates his plan, for the most part, from a mental ward, has Gwen Stacy kidnapped and then has her father betray the law in exchange for her safety, nearly takes over the world in the end... all while managing to casually sit back and drink coffee out of a mug labeled "Evil Genius".
Norman Osborn is also up there, playing both sides throughout season 1—getting paid to make supervillains to fight Spider-Man, and then getting paid to come up with the systems to contain them. In season 2 this continues, plus in "Accomplices" he carries out a beautiful plan wherein he gets the competition to demolish each other fighting over what is, ultimately, a worthless chip—earning himself half a billion dollars with no risk or effort. Oh yeah, and he was the Green Goblin all along, willing to break his son's leg to fool Spidey.
Danny Phantom has an intriguing one: Vlad Masters/Plasmius. He wants to marry Danny's mom, adopt Danny and kill Jack, not exactly in that order. A lot of his lesser plans work, but the main ones probably would if he had better control of his emotions and kept his priorities straight.
Darkseid from the Superman: The Animated Series and Justice League. Even though Superman usually won the day, he took every defeat (and victory) with the same steely expression. Even when Darkseid was beaten on his own planet, Superman threw his body to his slaves on Apokolips and said they could do whatever they wanted to with him. The slaves began to pick up their cherished leader and take care of him. While being carried off, Darkseid gave a confused and horrified Superman a parting line:
"President? Do you have know how much power I'd have to give up to be President? That's right, conspiracy buff. I spent $75 million on a fake presidential campaign. All just to tick Superman off."
Slade from Teen Titans normally falls on the Smug Snake side of things, due to his overconfidence and habit of grabbing the Villain Ball at inopportune moments, but in the three-part season finale "The End" he graduates to full Magnificent Bastard by orchestrating the downfall of a nearly all-powerful demon at no real cost to himself, getting his humanity back (which was his main goal all along) and doing it with style. Being voiced by Ron Perlman helps.
Demon Warrior: "Fool. You cannot hope to defeat pure evil!"
Slade: "Actually, I'm not such a nice guy myself." (activates hidden explosive and blows demon to cinders) "Don't bother getting up. I'll let myself out."
Derek Powers from Batman Beyond. Manipulated a city with his company, and only grew more deadly when he gained radioactive powers. Using his money, intel, and connections, he kept people under his thumb and proved to be a deadly opponent for the new Batman.
His son Paxton also qualifies, arranging for his father's exposure to the public and eventual demise despite Batman's best efforts to stop him. He does next to nothing in Season 2, but then again, why bother? He had already won in his first appearance!
V.V. Argost from The Secret Saturdays. Bold, manipulative, cunning, and brilliant, a master of misdirection with a showman's flair, more often than not he wins by the end of the episode and has proven to have a large array of technology and knowledge, as well as in impressive collection of cryptids and ancient artifacts, in his goal to Take Over the World. Indeed, he succeeds so well that it proves to be his undoing, as he is killed when he absorbs two forms of supernatural power which prove incompatible.
Mojo Jojo can be this at times. While his plans tend to be hair-brained, sometimes he's shown enough savvy and manipulation to casually perform things that people rarely notice until they happen (the "Powerpuff Girls Rule!" special is a fine example.) The movie played this straight.
There's also HIM, who always means business when dealing with the Girls. He tends to end up doing something that involves manipulating one of the Girls' feelings (Bubbles) or something on the grand scale.
Palpatine's responsible for engineering this massive war and will win regardless which side triumphs, either with the Republic as the Chancellor or the Separatists as Darth Sidious, with a powerful new sith follower (either Dooku or Anakin) as icing on the cake.
Ed Wuncler I is a combination of this and The Chessmaster. He is a fat and rich old man, who would normally not be the least bit threatening, but look at all he's done. And he does all of this just by being crafty, evil and obscenely wealthy. Magnificent Bastard indeed.
He opened a restaurant using illegal workers and Robert as his Unwitting Pawn, knowing full well the restaurant's food was so addictive it would turn the nearby park into a cesspool of crime and obesity, thus lowering the property values so he could buy the land for dirt cheap.
He tricked Jazmine, a 10 year old girl who started a lemonade stand, into being partners with him and then made it so that she ended up owing him money and allowed him to sell his own "cruelty free" lemonade.
He had his grandson Ed III and Ed's friend Gin Rummy break into people's houses so they'd buy his security system.
He not only had a girl fake a serious injury so Huey would quit the kickball team, thus restoring the curve, but then blackmailed him to play again.
Finally, he had Ed and Rummy set up a bomb in one of his buildings, and then calmly reveals when Huey and super agent Jack Flowers foil this plot that it was designed to inspire patriotism, sell merchandise, and make a movie about an obnoxious security guard who would have died in the explosion. And to top it off, when Flowers counts down 3 seconds before he shoots him, Wuncler calls PRESIDENT FUCKING OBAMA to stop him, then calmly tells them to let themselves out.
Rollo Goodlove, the self-serving black liberal activist.
He manages to come out on top in his first appearance, when he is revealed to be partners with Ann Coulter, who plays the part of a conservative nemesis to get "redneck money".
In his second appearance, he hijacks Huey's anti-BET campaign to promote himself, and then received a job from the network.
Carmen Sandiego. In the mid-90's cartoon version, Where on Earth is Carmen Sandiego?, she was as slick and suave as a female James Bond, but would steal priceless artifacts either just for the thrill or for a huge not-so-evil plan (in one episode, she stole several rare statues to make the worlds largest chess game) and would constantly bait and taunt the two detectives trying to catch her, all for the sport of the hunt (even though she was the prey.
Chase Young from Xiaolin Showdown, mostly during the second season in which he debuted, would meticulously manipulate events so that even if the monks won, Chase would benefit from it, mostly with regard to his plans to corrupt Omi. This lead to him, on several occasions, helping the monks in order to gain Omi's trust, as well as manipulating other villains to force Omi into situations where he would have to resort to underhanded tactics not approved of by his friends.
Sideshow Bob, however, is arguably the most obvious Magnificent Bastard in Springfield. His schemes are considerably clever, and typically just so happen to get thwarted by circumstances. Examples include: "Krusty Gets Busted", in which Bob frames Krusty for armed robbery, and takes over Krusty's show. He manages to convince almost everyone of Krusty's guilt, except for Bart and Lisa, who just so happen to uncover the whole scheme when Sideshow Bob says he has big shoes to fill.; "Black Widower", in which after being released from prison, Sideshow Bob convinces every Simpson except Bart that he has reformed. Bob then marries Selma Bouvier, who has made a lot of money in the stock market, so as to inherit her money. Bob also finds out that Selma tends to smoke after watching MacGyver, and that she has an impaired sense of smell. So he then decides that one day, to get the money, he will get up and leave while she is watching MacGyver, and leave the gas valve open so as to fill the room Selma is in with natural gas, without her noticing, such that when she lights up to smoke her cigarette when the show is over, the ignition will blow up the room she is in, killing her and leaving him with her money. The only reason this does not work is that Bart, who was already distrustful of Bob, also knew these things about Selma and managed to guess what Bob's plan was. "Cape Feare", in which Sideshow Bob manages to convince the parole people that he has reformed. Upon hearing of his release, the Simpson family flees Springfield to a houseboat in Terror Lake, but Bob manages to find their houseboat anyway. While the family is asleep, Bob disconnects the boat from the dock, and ties up all the Simpson family except Bart, including the pets. Then, cornering Bart at the edge of the boat, Bob is going to kill Bart until Bart convinces Bob to sing the entire score to H.M.S. Pinafore first. By the time Bob is finished singing, the boat arrives in Springfield, where the police are waiting for Bob and have him arrested.
Rava from Galtar and the Golden Lance. When she's assigned to take down Galtar, she actually succeeds in capturing him, and only ultimately loses because she also used the assignment to set Tormack up, tried to pull an I Have You Now, My Pretty and imprisoned Galtar when he refused, and Tormack and Galtar pulled an Enemy Mine to restore the status quo. In a series where the villains tend to be generally a touch more credible than most similar action cartoons of the age, Rava is still the most dangerous of them all.
Loki, first established during flashbacks in his first appearance and cemented when he explains how the 26 episode season was the result of his plotting during the Season Finale. Xanatos would be proud.
The second season features the machinations of the Skrull Captain America, who really utilizes people's trust in Cap well in order to further the Skrulls' plot for Earth. Preying on the Avengers' trust in the real Cap to keep them under surveillance without Iron Man to get in the way of plans, as well as dealing with the Hulk by having him voluntarily revert to Bruce Banner and letting Gen. Ross's Hulkbuster units detain him are two instances of this star-spangled phony's magnificence in bastardry.
Discord from the opening episodes of season 2. It doesn't hurt that he is both apparently inspired by and sharing actors with another magnificent bastard, Q. He's as old as — possibly older than — both Luna and Celestia, and the Avatar of Disharmony that ruled Equestria in an endless maelstrom of anarchy and madness and led to the discovery of the Elements of Harmony; yet he's also one of the Largest Hams available, while still being incredibly sneaky and evil. By the end of the first episode, he's played everyone for fools without even seriously trying, all the while enjoying every second and relishing in the mayhem and suffering he causes. He certainly doesn't fit the part about not being unnecessarily cruel, though, since that basically ishis goal. It's all summed up well in his fan-made Villain Song"Neverending Strife".
Queen Chrysalis is a more straightforward example. She shapeshifts into the exact lookalike of Princess Cadence in order to marry then bump off Prince Shining Armor so that she can rule Equestria. She's also an Emotion Eater who possesses the ability to gain power from other people's love. She intentionally invokes Cassandra Truth. Only ever acting Out of Character when Twilight is around, and making sure to get on Twilight's friends' good side whenever she's absent. Not only that, her "Out of Character" moments are so subtle In-Universe that only Twilight would notice. And she makes sure to have the excuse of "wedding stress" to fall back on in case anyone else calls her out. This serves to successfully paint Twilight as paranoid and jealous. Isolating her from her friends and potentially rendering The Elements of Harmony (AKA The Ponies "Fix All The Things" button) useless since they need all SIX bearers to function. She even let's Twilight see her brainwashing Shining Armour knowing that this will cause Twilight to freak out and give Chrysalis even more ammo to paint Twilight as rude and paranoid. And if that didn't work, she had the backup plan of sending a part of her army to fight the Bearers while the rest of her army secures the Elements themselves Another obstacle to usurpation that Chrysalis surpassed was Shining Armour and his shield spell, which could conveniently block all threats out of Canterlot. This was a spell that neither Luna, nor Celestia could accomplish. How do you overcome such an obstacle? Oh I dunno, how about impersonating his fiancé and sucking all his energy away? Keep your enemies close after all. not only that, she's also Genre Savvy enough to intentionally invoke Evil Gloating to buy her army enough time to break through Shining Armour's shield spell. Chrysalis's plan was almost perfect, taking out her biggest threats from most to least.
King Sombra in his two-part episode was certainly one in the past, at least, due to his Crazy-Prepared measures when hiding the Crystal Heart during his rule over the Crystal Empire. His returns cost him some of his splendor, but he's still a terrifying No-Nonsense Nemesis.
Lord Tirek is certainly one. He patiently manipulates Discord, a Magnificent Bastard in his own right, like a fiddle, and manages to successfully drain every pony in Equestria of their magic, including the Princesses and the Mane Six. He's also very good at playing Xanatos Speed Chess, catching up to current events and playing them in his favor. If it hadn't been for Discord's key, Tirek would have been unstoppable.
Spider-Man: The Animated Series gives The Kingpin and The Red Skull this treatment. The former is a crimelord who is behind almost every godawful thing that happens in-series, mastermind The Syndicate and the Insidious Six from the shadows, consistently evading incarceration, and frustrating Spider-Man at every turn. The latter's a Nazi spymaster who has backup plans for every situation, anticipates every contingency, and is only taken out via Captain America's Heroic Sacrifice.
The Hobgoblin retains his status as one from the comics as well. In his introductory two-parter, he's a hired mercenary working for Norman Osborn using goblin tech that Osborn created, and assigned to take out the Kingpin. Hobgoblin then doublecrosses Osborn in favor of working for Kingpin against him instead, but then is revealed to be a double agent still working for Osborn. But then he quadruple-crosses both Osborn and the Kingpin, taking over Kingpin's HQ and holding Harry Osborn hostage as leverage so that Norman couldn't stop him. And that's not getting into how effortlessly he plays with circumstances in order to derail Herbert Landon's project in the X-Men crossover two-parter or how he almost gets his hand on the dimensional transporter due to planting a spy in Kingpin's organization ahead of time, or even almost gets Felicia Hardy to marry him so that he can cease her wealth and resources. He unfortunately becomes subject to Villain Decay and The Worf Effect when up against the Green Goblin, but his run was good while it lasted.
While The Hacker suffered from Villain Decay, a new villain named Ledge becomes this when he tricks the Cybersquad, and Hackerizes them (minus Inez) and he Hackerizes almost all of the citizens in Sensible Flats,all to impress the Hacker. And, that he succeeded in hurting the Cybersquad more than The Hacker ever did made him a dangerous foe.
XANA wasn't initially much of this, but four seasons of evolution through Jeremy's abuse of the Return to the past made it gradually smarter and more powerful, turning it into a Chessmaster, then a Manipulative Bastard, and eventually going toward Magnificent Bastard territory. His status is best shown when he succeeds at destroying the core of Lyoko and takes possession of new Lyoko warrior William Dunbar to serve as his personal avatar to carry out his plans in the final season.
Belphegor, the main antagonist of the "Belphegor" French animated series could qualify as one. He's a Diabolical Mastermind, good at manipulating people and anticipating everything that's thrown at him, so he's never once caught or his identity revealed. You have a trap door in your house that he's conveniently standing over? Well too bad, he knew and had already made it unresponsive to your device! It helps that he has cameras installed almost everywhere in Paris, uses his mooks to spy, steal and kidnap for him (in the few cases he doesn't just do it himself), and apparently has enough money and access to high-tech gadgets and top secret, untested military technology, that can make a mad scientist drool at the thought. To actually make him lose his cool, you have to do something pretty terrible or disruptive to his plans, that could cause a really angry response. Otherwise, everything you do is met either with boredom, slight amusement or mild annoyance on his part.
Ghostfreak falls into this category too. He rode the DNA of another alien into the Omnitrix so that he could manipulate whoever ended up with it into doing his dirty work. It was heavily implied that he was behind the transformations that Ben didn't choose, a large amount of which resulted in Ben turning into . . . well, him; Ben acted meaner whenever he was transformed into him, which means that Ghostfreak was influencing him to some degree. He ended up summoning his minions to Earth while Ben was transformed into him (presumably controlling him entirely, which it was revealed he could do) with a plan to bring him back to life and turn Earth into a world of darkness just so that he could roam the planet without having to wear his outer skin. In the end, it was only his sheer arrogance that got him killed (twice) by exposing himself to sunlight without his outer skin, and the second time he went back into the Omnitrix while leaving his body to die. Oh yeah, and he played Vilgax in Alien Force, taking control of his planet just so he could get another chance to take Ben completely. The only way for him to be permanently destroyed was for the Omnitrix to be destroyed, which Ben did after getting the Ultimatrix.
Total Drama: Alejandro the Big Bad of World Tour, who was in some way responsible for almost every elimination, and plays everyone like puppets. Every character other than Heather was manipulated, exploited, or betrayed by him over the course of the season and he still manages to make it all the way to the finale.
The only other Scooby-Doo villain who qualifies is Ben Ravencroft, the charismatic book author descended from a witch from "The Witch's Ghost" movie. He has two things in common with Pericles: his status as this trope, and the fact that his downfall comes from his success in his ultimate goal. Oddly enough, he bears a striking resemblance to David Xanatos. Also, he's voiced by Tim Curry.
Generator Rex gives us Black Knight. From posing as a Reasonable Authority Figure, keeps her own true power hidden to use at later date when necessary, plays politics with the Consortium, and pulling off a successful Starscream to gain supreme power. She even admits that she wants power, believing that you have to admit it to yourself to get it. Throughout it all, she shows absolute Nerves of Steel, is soft-spoken, polite, acts as a Friendly Enemy despite being a ruthless foe, and so forth. Even when defeated, she ultimately escapes and becomes a Karma Houdini.
Greg Weisman, responsible for the above Magnificent Bastards of W.I.T.C.H., The Spectacular Spider-Man, and Gargoyles, has also produced The Light of Young Justice, a Legion of Doomnote consisting of Vandal Savage, Ra's al Ghul, Lex Luthor, Queen Bee, Ocean Master, the Brain, and Klarion the Witch Boy, with Ocean Master being replaced by Black Manta in Season 2 to erase any conception of the Legion of Doom as campy or incompetent. Unfortunately, some audience reactions indicate they may be too far in the other direction: when every scheme the heroes foil is actually a distraction from The Light's true plan, tension becomes reduced and the initial 'wow, what a twist, what an awesome group of villains' becomes 'sigh, time to watch the heroes waste their time and then not find out what The Light was actually planning, how exciting.' Well, at least until "The Summit", penultimate episode of the second season, in which the Light, while not completely defeated, certainly has their immediate plans blow up in their collective faces (with some help from the heroes), resulting in Black Manta and the Brain being captured, Ra's al Ghul being killed (albeit temporarily), and Vandal Savage and Klarion fleeing the planet aboard War World.
Eric Cartman from South Park has been known to be this on occasions. Despite being an ignorant slob who is shown to have little common sense in many things, he displays an uncanny level of charisma and social savvy. Very often, he is shown to be capable of manipulating hordes of people into going along with his latest audacious plan, whether they are aware of it or not, and treat it like sheer child's play. A few shining examples can be found where he staged the utter ruining of a teenager who scammed him out of sixteen bucks and manipulating Cthulhu itself.
Abraham Kane of Motorcity. He's a Villain with Good Publicity and lots of money, usually able to talk to the Burners through a screen (to make himself appear larger) rather than face to face, which makes him look impressive. The Duke of Detroit is also this at times, although more of a Friendly Enemy. As he's a Large Ham, he often likes to oppose the Burners in style, particularly with lots of lights and music, as well as firing at the Burners with limousines as ammo.
In an episode of Archer, Lana decides to get even on Cyril for cheating on her by having sex with everyone else in the office. At least that's what she tells Cyril. In reality, she makes all the guys pay her for the privilege of saying they had sex with her.
Gillette: [I'm] confused. If you told every guy the same thing, then they all know that none of them had sex with you, so they're all going to realize that they're all lying.
Pam: Hey, yeah!
Random office guy outside door: Wait a minute...
Lana: But remember: They're dudes.
Second random office guy outside door: What?
First random office guy: Uh... I had sex with Lana.
Second random office guy: Me too.
Gillette: Lana Kane, you magnificent bastard.
From the same show, Malory Archer is another anti-heroic example. She has a natural gift for playing both sides of a conflict in such a way that her actions only ever have consequences for other people. The only time it ever failed her was when Pam beat her up at the end of "El Secuestro".
Gravity Falls gives us Bill Cipher, a seemingly omnipotent being who has his grand apocalyptic plan completely mapped out from the start, has been putting the pieces into place for years, and doesn't allow any apparent defeat to be a setback, only a delaying of the inevitable. Bill is fond of making deals with people in which he gives them something they want or think they need, and in return, they can be used and likely screwed over by him later so that he can reap even better benefits. As it's said, he would use or possess anyone in order to get what he wants, shown clearly when while possessing the time traveler Blendin, he takes advantage of a distraught, emotional Mabel and tricks her into giving him a dimensional rift belonging to their uncle, and then smashes it, creating the tear between the two worlds, bringing about Weirdmageddon. He only appears in a few episodes, but his presence is felt even when he's gone, and while undeniably diabolical and sadistic, he's also hilarious and great fun to watch and speculate about.
In Star vs. the Forces of Evil we have the evil, slick, cool-headed Patrick Bateman-esque monster known only as "Toffee". First he gets Ludo to hire him simply by making him believe that he did hire him, and proceeds to advise a fairly competent Evil Plan that's clearly truly intended to test the capabilities of both Star and her wand. He then skillfully manipulates the events of "Mewnipendance Day" resulting in Ludo firing Buff Frog. Furthermore, he manipulated Ludo's army into throwing Ludo out after a situation arranged as to make Ludo look especially bad, and becomes their leader instead. And it's implied that he'd been waiting a while for Ludo to put on the display of weakness he needed to convince the monsters to rebel. During all this time he also made sure to stay out of Star's way so that she wouldn't notice him, and the fact that Marco and Star aren't even aware of his existence until the season 1 finale proves he's savvy enough to keep himself a secret. At the end of Season 1, Toffee gets what he wants: the wand is destroyed, and is only partially reformed thanks to a heroic unicorn, but with one broken shard still missing. The broken shard, and the skeletal remains of Toffee's hand, form a new wand which Ludo finds. Toffee then manipulates Ludo and eventually takes over his body.
The Choten from Kaijudo. Few tropes could better define The Choten. He is an extremely sick person, but there is no doubt about him being incredibly badass. As he shows at various points in the series, but especially the first season finale, he knows how to roll with defeat like a real chessmaster too.