Pokemon Black And White brought us a literal Smug Snake in Snivy, the Grass-type starter PokÚmon. As if its actual name doesn't make the point clear enough, it quickly started being called "Smugleaf". And it only gets smugger throughout its entire evolution line. There's a reason its final evolution Serperior is nicknamed "Smuglord", and its actual name certainly makes the point too. Even its PokÚdex entry agrees. Ken Sugimori has stated that Snivy's personality was meant to be similar to that of European (particularly French) nobility, so that's why.
That being said, his smugness is somewhat justified due to being incredibly Dangerously Genre Savvy. If it wasn't for his attitude, he'd probably be a Magnificent Bastard. And even then, the fans still Love to Hate him. Also, when he returns in the sequel he's got pretty much no ego left to lose.
Zetta from Makai Kingdom is another good guy example, though far less sympathetic and Played for Laughs. Despite declaring himself the "Most badass freaking overlord in the universe" about once a scene he spends most of the game powerless, surviving mostly on the charity of people he regularly insults. The game levels things out by making him a regularly mocked Butt Monkey.
And then there's King Drake III, whose smugness could probably clog up a black hole. It goes hand in hand with him being a Harmless Villain, ensuring that nobody takes him seriously. Pram ends up booting him out of his own netherworld off-screen and nobody cares.
Rosencrantz from Vagrant Story is a smug bastard all the way, who thinks he has the secret of Lea Monde all figured out...and then Ashley whips his ass, and hardly anyone seems to care. Rosencrantz has to yell yield, and Ashley mocks him for it. Not only that, but the game's real Magnificent Bastard gets a shot. After Rosencrantz has ambushed Sydney and Ashley, Rosencrantz demands Sydney name him his heir. Sydney calls him a "worm", and Rosencrantz chops off Sydney's arm. Sydney, bleeding Black Blood, stands up and reattaches his arm. He then demonstrates to Rosencrantz that not only is the man not immune to Sydney's magic like he thought (by making him think he was holding Sydney's severed hand), but Sydney had been manipulating him the entire time. And in the end, Sydney doesn't even kill Rosencrantz. He lets a giant six armed statue of Kali do it for him. Truly, in case you had forgotten the real Chessmaster and Large Ham in the story, Sydney does not fail to remind you that he was eating the scenery first.
General Sarrano from Bulletstorm is a walking bottomless pit of arrogance, foul language, callousness, and pure evil. He uses soldiers like Grey and Ishi to carry out genocide and assassinations and then pretends to be angered by the casualties left in their wake after they take down his prized warship near the beginning of the game.
Dahlia's status as this was likely intentional, given that Mia and Phoenix actually get rid of her by pointing out what a failure she is. Ironically, she actually did more harm than some of villains who are closer to qualifying as Magnificent Bastards, like Matt Engarde. It could be argued that this is Truth in Television. The chances of being caught for a crime exponentially increase every time a murder or similar crime is committed. Expert criminals will want to avoid this by minimising the targets, causing less harm. An example follows: Manfred von Karma used someone to kill a person just to wreak revenge on Miles Edgeworth. On the other side of the scale, Joe Darke had no real criminal plans whatsoever and became a mass murderer.
Daryan Crescend from Apollo Justice laughs disdainfully at pretty much every accusation Apollo throws at him, convinced it isn't enough. As a result, his breakdown is truly satisfying.
Also from Apollo Justice is Alita Tiala who at first acts as the eager fiancee of the defendant, until she reveals that she's a petty Gold Digger who only hired Apollo because she was under the impression that the office he's employed under is a third-rate and questionable law firm that will get the defendant convicted for sure. Boy did that backfire spectacularly. It's satisfying to wipe that smug grin off her face.
Erol is the Draco Malfoy of the the Jak and Daxter series - he's a smug, arrogant jerk who gets in Jak's face nonstop from the moment his character is introduced. He gets even worse after his "death" and resurrection as a cyborg in the third game.
Stratos from Sacrifice, who is extremely self-centred, smug and disdainful towards most of the other gods while barely hiding it under a veneer of civility. He has rather overt aspirations towards monotheism, and turns out to be the mastermind behind the main plot, which (unless you serve him), eventually derails beyond his control and kills him.
Tohru Adachi, the true killer of Persona 4 is every bit the Smug Snake Ikutsuki was. While his inital scheme, which involved manipulating Namatame into committing the rest of the killings and leading the heroes into a wild-goose chase against himwas quite clever, he quickly devolves into the personality of a Smug Snake when the heroes discover his plan and give chase after him, whereby his true personality as a mocking, arrogant Nietzsche Wannabe is finally revealed. Also, in further true Smug Snake fashion, it turns out that he himself is being manipulated by higher powers beyond his control, who are in turn being controlled by an even greater power. In other words, the puppet of another puppet. Furthermore, also spoiled his seemingly clever scheme not once, but twice throughout the game. The first one is easy enough to miss. When Naoto is reading off the list of victims found in Namatame's truck, he simply states "Whoa. That solves everything." Without even possibly even knowing what Naoto is talking about. The second time is much more obvious. When he cries out "Namatame was the one who put them all in!" He supplies all the evidence the heroes need to prove he is the killer.
Zexion from Kingdom Hearts: Chain of Memories. He's very overconfident in his strategic and manipulative abilities, but none of his schemes work out like he wanted them to. Appropriately enough, he winds up being (indirectly) done in by the game's realMagnificent Bastard, Axel.
Most villains from the Atelier Iris series, the biggest example being Mull. His Expy, Crowley, was thankfully a lot closer to being a Magnificent Bastard, but still didn't quite make it.
Most of the non- and post-Dracula villains in the Castlevania series, such as Graham Jones in Aria and the cult leaders in Dawn, come off as Smug Snakes vainly attempting to fill the Count's shoes o' evilness. Also, Walter in Lament Of Innocence, primarily because his motivation for doing evil was being a bored, unkillable vampire asshat. Can't get much more smug than that. They all have a distinct tendency to get effortlessly manipulated by Dracula and pro-Dracula minions such as Death. Mostly-averted by tragic-backstory-vamp Brauner, and Isaac, who's far too... entertaining to qualify.
Dmitrii Blinov from Dawn of Sorrow at least makes an effort, pulling of a combination of I Surrender, Suckers and My Death Is Just the Beginning, before coming back to life and successfully copying Soma's Power of Dominance in a surprisingly successful gambit. He was more of a "Magnificent Bastard in the making", right up until he ended up dying again.
From Order of Ecclesia comes another partial-aversion: Barlowe does a fine job of hiding his true allegiance to the Dark Lord, effortlessly manipulating Shanoa into obtaining Dominus so that, by using it, she can resurrect Dracula. And, when he reveals his True Colors, he isn't that smug about it, just real effin' crazy. He ends up resurrecting Dracula anyway even after being defeated.
Nicholai from Shadow Hearts: Covenant tries so hard to be a Magnificent Bastard. He's charismatic, scheming and utterly selfish, and loves to taunt you from just outside your reach. He sets up deals with every evil faction in the game so that whoever remains standing at the end, he should achieve his goals. He even contracts the power of a god! Unfortunately for him, he doesn't quite count on Yuri kicking the crap out of everyone, his his plan to release the Malice of Apoina Tower comes off as petty revenge, and he ends up getting completely outmaneuvered by someone even more scheming. And the completely undignified way in which he finally bites the dirt.
Shinji Matou from Fate/stay night. In all three routes (Fate, Unlimited Blade Works and Heaven's Feel) he's shown as an overconfident idiot who tries to win through manipulating more powerful characters such as his servant Rider, Gilgamesh and Sakura and it alwaysturns out badly (and sometimes bloodily) for him. In reality, he's being manipulated, by his grandfather Zouken. This is most obvious in Heaven's Feel (where his actions form most of the impetus for Sakura's gradual Sanity Slippage, culminating in his eventual death and her Freak Out), but is also true in the other two routes.
Gilgamesh is this as well. Oh, sure, with his enormous strength and power he could easily have become a much more successful villain, but he's just so damn egotistical that it winds up costing him dearly in each route he appears in, particularly in the UBW route, where he foolishly underestimates the power of Shirou in the end.
Vaati in The Legend Of Zelda The Minish Cap comes off as a Smug Snake as well, with his digitialized "Mmmhm mhm" laughter, it doesn't help when one realized He used to be an itty bitty Minish, taking away a good chunk of his 'evil aura' - Minish Vaati is just too cute!
Dr. Wallace Breen of Half-Life 2 fame. Acting as the puppet governor for the Combine, Breen keeps spouting out propaganda about the good intentions of "our benefactors" throughout the game (despite overwhelming evidence to the contrary) as well as making disparaging remarks on how Dr. Freeman "has created nothing". He is not even above threatening the transhuman Combine soldiers with "permanent off-world assignment" as a punishment for failure or, for that matter, the entire human race with extinction if they do not comply. He also seemingly betrays his own Mole within La RÚsistance, Dr. Mossman, refusing to make a bargain for Dr. Vance's life. Breen keeps gloating about how Freeman will be "destroyed in every way possible and some ways that are essentially impossible" even when he is about to escape through the Combine portal. He is apparently killed as Freeman damages the dark fusion reactor, causing the portal to collapse.
Alternate Character Interpretation suggests he genuinely believes that sucking up to the Combine is the only thing that will stop them from wiping out mankind. The resistance believes Gordon is the only thing that will stop them.
Saleh from Tales of Rebirth. This guy is presented as a Badass member of the Kingdom's Elites, but all he does is approach the heroes, taunt them, and do nothing. Later on, after being lectured by Tytree, he comes in denial that there is no way that the human heart can defeat him. So what does he do? Taunt the team even more rather than kicking their ass. Add to the fact that he's all doing it For the Evulz, he's as smug as you can get.
Grand Maestro Mohs from Tales Of The Abyss is a high-level member of the Corrupt Church with designs to plunge the world into all-out war "for its own good". He's also a Villain with Good Publicity (even amongst some of your party members), and legally untouchable because he never touches anything directly. He is as such free to spend most of the game's story smugly plotting on the sidelines and looking down at both ally and enemy without suffering any personal backlash, even after performing the game's arguably biggest Kick the Dog moment by killing Ion. He's finally killed after devolving into an Ax CrazyOne-Winged Angel.
Gary Smith from Bully is the Failed Magnificent Bastard + Villain Sue type of Smug Snake. For his Smug Snakery to work, it requires 1) that everyone in the game take everything that comes out of his mouth at face value, 2) putting aside the fact that he has a reputation as a sociopath and common sense says ignore him, 3) that protagonist Jimmy spends most of the game insisting that going after Gary "has to wait" rather than going after him. And then, most importantly, 4) whenever Gary makes an appearance, all protagonistic figures must lose all ability to take action, period, and devolve into a stuttering stammering mess until Gary is done talking and has left the area.
Sengoku from Yakuza 2 is an epic Smug Snake, from his gold suit and retro sunglasses all the way to his camp personality and permanent toothy smile. Spending his time blackmailing your contacts and minor allies into turning on you, he proves so irritating that he eventually ends up being taken out by his own Dragon and thrown off a building. You can't help but thank him for the service...
Both Waylon and Admiral Greyfield in Advance Wars: Days of Ruin. Waylon fights on Greyfield's side against your army just because he feels like it, and Greyfield's fully convinced that anyone who doesn't conform to his worldview doesn't deserve to live anyway.
Advance Wars 2: Black Hole Rising has the appropriately-named Adder, who fights dirtily, has utter contempt for most of his enemies (and tries to persuade the one he does respect to join Black Hole) and revels in the crushing of civilians. Every defeat you inflict upon him is wonderfully cathartic. Contrast with his superior, Worthy Opponent Hawke, who tempers his villainy with competence and a healthy respect for his opponents.
This gets turned on it's head when, at about 10% HP he uses "Wrath of Frostmourne" and procedes to blow yourraid apart, going into a monologue about how his entire plan from the start was taunting you into chasing him and crafting you into an ultimate general for his undead army. Were it not for Tirion Fordring busting out of his ice prison, he would have succeeded.
He gets little development or even screen time, but Angelo probably qualifies based on the one scene. He's Sarevok's lackey who takes over the local law-enforcing mercenary company when Sarevok's plans to get its real leaders out of the way go into motion. When you are arrested for murders you were either framed for or goaded into actually committing by Sarevok, he's more than happy to glibly pronounce you the death sentence for a list of imaginary charges besides murder, clearly enjoying the abusing of power. He even gets a potential Kick the Dog moment in that if you mouth off to him in a way that manages to actually annoy him, he'll have a random party member killed on the spot. He's even annoying in the final battle, as he charges you and starts somehow exploding in fireballs repeatedly.
Even more so, Isaea Roenall in the next game. He oozes it. "Don't take it so hard, I'm just... better than you. Oh, and feel free to lodge a complaint with the proper authority. That would be... me." He too abuses his military position to get away with anything, including kidnapping one of your party members when she doesn't want to go trough with their arranged marriage. Luckily, the ensuing quest lets you bring him down in flames. This is very satisfying.
Edwin, a party member. His dialogue clearly indicates that he thinks he's a Magnificent Bastard and he almost never shuts up about his masculinity and being a Red Wizard. Problem is, he doesn't realize that he's one of the designated comic relief characters...
"Baron" Ployer, an ex-slaver that was exposed and humiliated by Jahiera and is now plotting a harebrained revenge scheme; Galvarey, a corrupt Harper that seeks to use the PC's status as a Bhaalspawn as a bargaining chip to increase his status; and Dermin, Jahiera's former mentor who was in on Galveray's schemes and is just as bad as he was.
Ramon Salazar from Resident Evil 4 fits this trope to a T. He's a smug elfish character, who constantly condescends Leon Kennedy by calling him by his last name and ensuring that the next trap will surely kill him. The further Leon gets into the castle, Salazar starts to lose his smug sarcasm, and yells "JUST DIE, YOU WORM!". The last battle with him is so annoying and deliberate, several players simply use the one-hit kill rocket launcher to be rid of his irritating ass.
Ricardo Irving from Resident Evil 5 is the spiritual successor to Salazar, except taller and with an even more irratating boss battle. An arms dealer with zero scruples or loyalty, he happily seeks to profit by selling biological weapons to the highest bidder, even when that highest bidder intends to kill off nearly all life in the world.
Ozwell E. Spencer, Big Bad and The Man Behind the Man to the whole series is one of these as well. He wanted to be a god, but had no idea how to go about doing it, so he hired the various Evil Geniuses who make up the antagonistic characters, and let them research at will, hoping one of them would create a way for him to achieve his godhood. In a series full of brilliant or horrifying bad guys with One-Winged Angel forms that are the stuff of nightmares, Spencer stands out as an Evil Cripple and The Man Behind the Curtain, who waits far too long to put his plan into action, and eventually sees it hijacked by his former protege, Albert Wesker. Smug, condescending, and not nearly as smart as he thinks he is, the old man is one of these to the end.
Duke Snakeheart from Final Fantasy Tactics A2. As if his name didn't give it away, he's a smug bastard who thinks he has it all planned and tries to do things his way, in spite of the other Duelhorn members objecting his actions. In the end, he admits to being the one that leaked Duelhorn's battle strategy and poisoned the girl Maquis saved for no apparent reason. In fact, during the fight, he says that he trusts no one but himself. He only questions the error of his ways once you defeat him.
"Queen" Valentina from Super Mario RPG shows many traits of your classical Smug Snake, including an over-inflated ego as well as a penchant for treating her underlings (specially her fat, feathered punching bag of a dragon Dodo) and everyone she encounters with as little respect as possible.
Everybody not on the Tokugawa side in Samurai Warriors sees Ieyasu as a Smug Snake.
Every significant villain in Baten Kaitos Origins except Baelheit himself has a tendency to trip over this trope at one point or another, mainly because of their tendency to rely on advanced weapons/magic as a crutch to take out people far stronger than them, then act completely flabbergasted when it finally doesn't work. All arma-users also seem motivated exclusively by arrogance, until their various heel face turns, and Wiseman seems convinced that his magic is the most powerful force in the universe until the very end of the game.
And in the end, his schemes don't matter. Because the Ankharan Sarcophagus he spends the whole game trying to get not only never had an Antidevelluvian he could commit diablerie on, but the mummy has long since been switched out for a bomb set to blow on whoever opens it.
King Shagall from ''Fire Emblem: Geneaology of the Holy War'.,
Also Sonia from Fire Emblem: Blazing Sword, who believes herself to be the most powerful mage and heartlessly manipulates her husband, the guy's family and her adoptive daughter Nino to please Lord Nergal. While she is a powerful Dark Action Girl, her arrogance is such that her daughter's partner Jaffar would rather have a Heel Face Turn than obey her orders, and in the end either Limstella simply leaves her to die in disgust, or Nergal finishes her off.
Ephidel and his perpetual and extremely irritating grin from the same game. Fittingly, he's probably the most utterly disgusting character in the game, at least among those who aren't out of their minds.
Pablo, Riev and specially Valter from The Sacred Stones. The first one only thinks "Money, Dear Boy" and tries to bribe everyone in his way; the second is a Sinister Minister worshipping a Dark God without reason at all, and the third is a monstrous Blood Knight who wants either to bloodily kill Ephraim or keep Eirika as his Sex Slave.
Narshen from Sword of Seals fits this trope almost perfectly.
Lekain from Radiant Dawn is almost capable enough to be mistake for a Magnificent Bastard. A high-ranking member of Begnion's Senate, Lekain arranged the Serenes Massacre and assassinated the previous Apostle, placing Sanaki, whom he thought he could easily manipulate, on the throne in her place (while making sure Sanaki's half-sister/the real heir did a dissapearing act). He's also The Man Behind the Man to Izuka and Naesala, and it gets to the point where if something bad happened to a character it was probably Lekain's fault. However, at the end of the day, he's a Big Bad Wannabe and an Unwitting Pawn of Sephiran the game's real Big Bad. The business with Sanaki really backfired on him.
Strider: Matic, especially in the manga for his kick the sheep affair
The Guardian from the Ultima series, at least in Ultima 7: The Black Gate. He constantly taunts, insults and annoys the Avatar in feeble attempts to scare you off, all the while you uncover his plots, undermine the Fellowship, gather plot coupons and smash the prism generators. Even though he's fully aware of everything you do he never bother to alert the Fellowship to the fact that you are not their friend, his own Dragon Batlin keeps treating you like a clueless dupe right up until you try to interrogate him with the prism cube, and when you finally pull out your ace and foil his plan, he's downright shocked that you were able to stop him.
Amon from the Lufia series. He's the Sinistral of Chaos, making him the most qualified to become a Magnificent Bastard when compared to the Sinistrals of Destruction, Death, and Terror. Unfortunately, he's also the second of four Sinistrals. This means that he doesn't show up until the heroes have become strong enough to kill the God of Destruction, and he's not high enough up the ranks to be the Big Bad or even The Dragon. He generally gets off one good plan, and then gets defeated quickly enough to get the real Big Bad more screentime.
Idura from Lufia II: Rise of the Sinistrals, and especially the remake Lufia: Curse of the Sinistrals, manages to completely overshadow Amon in this regard. He's just as overconfident, but doesn't have the justification of being a God. Instead, he spends most of his time laughing while kidnapping babies and girlfriends. Appropriately, he develops a rivalry with the Boisterous Bruiser of the team, and most of his "brilliant traps" are overcome with brute force.
Given how much backstory and justifications he's been given in the canon of Dragon Age, fans are still arguing whether this applies to Loghain, but one of his lackeys, Arl Howe is a golden example of this trope. Not only is he overconfident, arrogant and rude towards the PC, he even crosses the Moral Event Horizontwice on the very basic game that plays out to all origins and completely vaporizes it in Human Noble origins:you find out that Howe earned his title as Teyrn of Highever by slaughtering the former noble's family, despite them being his old friends. That incredibly smug smile and Tim Curry's voice only strengthen his position as one of the meanest characters (and as the most satisfying bossfight) in the whole game.
Arl Howe is so bad that after his death, the player can overhear a conversation regarding his funeral between two nobles, one of whom had been a friend of Howe's in their youth. The other noble asks why he isn't going to the funeral and if he'll let Howe go unmourned, to which the friend replies that the only thing worth mourning is that Howe didn't die years ago.
Sister Petrice of Dragon Age II, a backstabbing, conniving fanatic whose attempts to start a war with the Qunari from behind the scenes keep getting derailed by her utter contempt for her would-be accomplices and her inability to shut up about her racist beliefs at the most crucial moments.
However, Kirkwall does get into a war with the Qunari, exactly as Petrice wanted. But Petrice only proved to be one-third of the sparks that ignited the fire; the other two were the city petitioning the Arishok to return a couple of recent elven converts, and the Tome of Koslun being stolen once again. So this trope still applies to Sister Petrice even if Petrice ultimately succeeded: Petrice is too incompetent to start a war with the Qunari on her own; a couple of events beyond Petrice's power to influence had to occur first.
Hazama/Terumi from BlazBlue might as well be the poster boy for smug snakes. The man is constantly associated with snakes, almost never stops disregarding even the biggest threats around him as he is confident they can do nothing to stop him, his weapon is a chain with a snake head called Ouroboros which is a symbol traditionally represented as a snake biting its own tail, and at the end of Continuum Shift, Takamagahara actually refers to him as "The Snake". However his smugness is entirely justified in that he is using magic to learn and retain knowledge of every single possibility in the time-space continuum. Not even otherwise omniscient Takamagahara could do that.
What keeps him from being a full-blown Magnificent Bastard is that he easily loses his cool if, in any at all way, his plans are disrupted, he is not being regarded as the centre of the universe or his "truth" is called into question note a true Magnificent Bastard would keep his cool even if the proverbial seat of his pants is on fire - a spectacular meltdown is expected only if every once-viable outcome now leads to defeat. His knowledge of the time loops and continuum shifts is meaningless if he fails, or refuses to understand the motivations of his victims - half-formed layers of backup plans can only carry one so far before an exploit is found. Case in point: Slight Hope.
Sovereign is very competent, but isn't above Evil Gloating when he finally meets Shepard.
If you don't invest in Charm/Intimidate points, Saren comes off as one too (again, however, a competent one).
The second game has Warden Kuril, who turns out to be Too Dumb to Live when he tries to capture Shepard's crew while still letting them keep their weapons.
The Illusive Man jumps off the slippery slope in the third game, but being voiced by Martin Sheen helps him maintain some gravitas even as he loses his mind in the endgame. His new henchman Kai Leng, on the other hand, is possibly the biggestjerk in the whole series.
Captain Shannon from The Orion Conspiracy turns out to be this. He had some potential for Magnificent Bastard. He murdered Danny by having a concussion charge blow up, damage Danny's spacecraft, and it falls into a black hole. Shannon had a wife, and he blames the main character Devlin for her death. Danny's death accomplished two things...1. It got to Devlin and hurt him, and 2. It made Devlin come to the space station, where Shannon would be able to deal with him on his terms. Then he hideously murdered Kaufmann to frame Devlin. He had Devlin tossed into a makeshift prison, and said that he would hand Devlin over to the authorities once they arrive. It is revealed later that Shannon planted a bomb in the shuttle that Devlin was going to be transported in, and that it would have blown up once it got two kilometres away from the station. Fortunately, Devlin escaped the prison before that happened. Then Shannon personally confronted Devlin, held him at gunpoint, and smugly (ha, ha!) confessed to the murders and the reasons for committing them. Too bad for him he did not count on Meyer (who he was on bad terms with) overhearing the confessions and jumping him.
Lt. Blake and his boss, Captain Perry, in Heavy Rain would have this kind of attitude around Norman Jayden. Count on the likes of Dr. Adrian Baker and Mad Jack.
Eva-Beatrice of Umineko no Naku Koro ni is incredibly arrogant as she treats her allies poorly whenever they fail to entertain her and acts like a jerk any time that she feels safe, and she gets reduced to a screaming mess when things don't go the way she wants them to.
Similarly, Higanbana No Saku Yoru Ni gives us Higanbana, who was introduced as this in EP1. Then again, that's just the first episode, so...
Needless to say, Kanamori manages to be even more of a Smug Snake than Higanbana ever does, to the point of going insane at the best of times whenever he gets away with something.
Fear Effect presents Madame Chen. She is a pimp who runs a brothel behind a restaurant. She is a Card-Carrying Villain. She can turn into a demon, and happily admits to being "a bitch from hell" when Hana calls her that. She never changes her attitude, even when Hana kills her off and she ends up in hell. Okay, she did give Hana a doll that allowed Hana to meet her literal inner child, but it didn't seem to redeem Madame Chen at all.
L.A. Noire has a lot of corrupt officials and cops of this, but Roy Earle takes the cake since he's a Karma Houdini.
Henry Leland from Alpha Protocol is a Corrupt Corporate Executive who spends the entire game smugly debriefing you of your misadventures. While he is also Affably Evil, it's clear the main reason for this is because he thinks he's already won and is now just taking the time to politely rub it in your face. Unless you take his offer of We Can Rule Together and decide not to screw him over in the ending, Mike outplays him quite handily.
Kuja from Final Fantasy IX, is a genuine threat—but not only is he obscenely arrogant and cruel, he's ultimately unable to overcome his fear of death. Essentially, he has the mind and air of a wicked genius, but the temperament and personality of a frightened, spoiled child. This mainly shows up in the latter half of the game. It's played Up to Eleven in Dissidia: Final Fantasy.
Caesar in Fallout New Vegas is rare strain of this trope as he's not only competent, but the game's Big Bad; he's just not as competent as he thinks he is. He doesn't even make a token effort to sway the Courier's loyalties if you oppose the Legion, he openly insults your intelligence if you ask about his beliefs, and if you try to release Benny he blackmails you into killing him, even though it will likely only give you another reason to hate the Legion.
Like Caesar, Jack is another example that is genuinely competent enough to hold his own as the Big Bad, to the point where, for a large portion of the game, he's actually righton that first part.
Matt in PAYDAY: The Heist pulls a Face Heel Turn on your crew in the middle of the heist by killing one of your members and then locks you inside a room as he runs off with the money. He taunts you before leaving and even after you catch up to him when he gets into an auto accident, he refuses to come out and says he rather have the cops deal with you. The crew decides to light the van on fire to burn him out and when he comes out, he begs to be let go while the crew drags him to the rendezvouses point threatening that they may cut his arm off to detach the briefcase of money he has on his arm.
Most of the villains in Radiant Historia, but especially Queen Protea. She's petty, vain, incompetent, has an extremely inflated sense of her own importance, disregards her stepdaughter completely, kicks any dogs within reach, and is so oblivious to everything actually going on that she's effortlessly manipulated by her advisors. When the party actually confronts her in one timeline, she refuses to believe her army could possibly be losing when several of the enemy commanders have just burst into her throne room, and doesn't actually get it through her skull that she should be worried until Stocke is actually holding a blade to her neck.