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Draco Malfoy. He gets better, but not before being completely broken.
Draco's dad Lucius is one too (apparently being a Smug Snake runs in the family). He's very smart and has the polish of a Magnificent Bastard, but his arrogance and certainty that he can get away with anything lead to some sloppy mistakes. By the end of the series both Malfoys turn out weirdly pathetic after they are forcibly shown that an Evil Overlord does not a good houseguest make.
Justified by the fact that his making so many horcruxes left him decidedly... unstable. The young Tom Riddle is shown to have been a much more smooth and successful schemer, largely because he knew how to keep a cool head and didn't yet look like a monstrous snake-human hybrid. At any rate, whenever anyone talks about any version of Voldemort's genius, they're generally referring to his magical genius, which is unquestionable, rather than his tactical genius, which as has been mentioned above is rather lacking.
James Potter was supposedly this as a teenager. Problem was that he was genuinely talented and intelligent and actually pretty good (if not bigheaded at times. He grew out of it (even becoming Head Boy of Hogwarts in his final year).
Severus Snape plays this straighter though was more subtle about it. This was occasionally seen in adulthood albeit more through his attitude on others.
Considering he and his enemy James were both very talented young wizards, this probably crossed over into Smug Super.
Artemis Fowl from the book series of the same name is certainly a genius but his snarking is usually outdone by most of the other characters, he is physically weak and most of his plans fail due to him either having a crisis of conscience or due to his own overconfidence and incompetance. In short, for a criminal mastermind, this guy is overrated.
Minerva Paradizo from Artemis Fowl and the Lost Colony is trying to be a Magnificent Bitch and would be as she's easily as clever as Artemis and significantly more ruthless however she is obedient to her patronising and overprotective father, is easily outwitted by Artemis and suffers Villainous Breakdown when her own Dragon rebels against her.
Really this could be the hat of the entire Lannister house, even the more clever members of the family who qualify as Chessmasters in their own right are still so odious and preening it's hard to root for them. Jaime gets better, and Tyrion for all his faults seems more like an Anti-Villain.
Lord Petyr "Littlefinger" Baelish seems like a Smug Snake to most of the other characters, but this is a smokescreen to hide what is actually a subtle Magnificent Bastard, who has apparently single-handedly organized the War of Five Kings as well as the assassination of two kings, while simultaneously organizing the rise of a new queen... his protegee Sansa Stark.
In every appearance of Viserys, the book contrasts his attitude ("You don't want to wake the dragon, do you?") with the reality: he's a spineless, pathetic little man who bullies his sister Daenerys because there's nobody else even close to being weak enough to let him get away with it. When Dany develops enough strength to resist him, Viserys mentally collapses and gets himself killed within a few pages.
Theon Greyjoy could be the poster boy for this trope. At least until A Dance with Dragons, where Ramsay Bolton has tortured him into insanity - he's a thoroughly broken shell whose mind slides between his current identity as 'Reek', Ramsay's completely subservient and terrified slave, and his former identity, Theon, who bears little to no resemblance to his former self.
House Frey consists of so many Smug Snakes it could easily be considered their hat. There are a few exceptions to the norm within their family, but they all fade out of prominence as the more evil members take charge.
In the Dragonlance novels, Quarath, the Evil Chancellor to the leader of the Corrupt Church fits this model. His own ambitions for power and wealth are compared to the epic confrontation between actualMagnificent Bastards Raistlin and Fistandantilus of which Quarath is completely unaware. Ended up being squashed by a pillar as his temple collapsed when his master pisses off the gods that Quarath had stopped believing in by this point.
In the later War of Souls trilogy we get Morham Targonee, Lord of the Night, who despite his impressively evil sounding title is a scheming accountant who happened to be in the right place at the right time to seize power. When the local Dark Messiah shows up and steals his job, she punishes him in what is perhaps the worst way a Smug Snake can experience- by forcing him to realize his own cosmic insignificance before killing him.
Cosmo Lavish from the Discworld novel Making Money is an obsessed fan-boy of Vetinari, who is an actual Magnificent Bastard. He tries extremely hard to be just like Vetinari, trying to get his old clothes and practising his eyebrow-raising. He eventually goes crazy, thinking he really is Vetinari, and gets committed to an insane asylum, which apparently has a whole ward dedicated to people who think they're Vetinari. His sister, Pucci Lavish, isn't much better.
Lord Hong from Interesting Times is another, though less funny and less pitiful, example. He is, admittedly, Awesome by Analysis and the Big Bad of the novel, so not a pure specimen. He does, however, exhibit the trademark snarky attitude, overconfidence and pre-failure breakdown.
There's also the Supreme Grand Master, a.k.a. Lupine Wonse from Guards! Guards!!, who vastly overestimates his own power in summoning and controlling the dragon which terrorizes Ankh-Morpork, in that he can summon it but has no means to control it.
Dragon King of Arms from Feet of Clay, the mastermind behind the plot to poison Vetinari and replace him with a puppet ruler. His plan falls apart because he arrogantly underestimates Vimes and the rest of the City Watch.
The emperor of France, Napoleon Bonaparte, in War and Peace. The characters take up at least a third of the book talking about, predicting the actions of, or plotting against him. When Prince Andrei and later when Balashov, an emissary of the Russian emperor, finally meet him, they're both struck by how disappointing he is compared to his reputation. He's purposefully portrayed this way.
The title character of A Coffin for Dimitrios is a good fit, being a clever schemer, but such an unpleasant treacherous thug that he's completely unlikable. Also notable is that he ends up addicted to the same drugs he sells, something which would never happen to a Magnificent Bastard. Interestingly, the character might have been an inspiration for Keyser Soze of The Usual Suspects, who by contrast is definitely a Magnificent Bastard.
Vidal Vordarian from Lois McMaster Bujold's Vorkosigan series. He wants to run Barrayar, but is effortlessly and unintentionally defeated in his attempt to do it legitimately by Aral Vorkosigan. So he tries a coup, but fails to capture the true heir or assassinate the Regent. He gets the ruling council to go along, but only at obvious gunpoint. And then he loses his head to Vorkosigan's wife. His "greatest" achievement is his implied rape of the dowager Empress, who he marries (again, obviously by force). Smug Snake indeed.
He doesn't actually marry her. He just announces their engagement.
Frederick Chilton from Red Dragon and The Silence of the Lambs, who comes across as a bully as head of the Chesapeake State Hospital for the Criminally Insane. In Silence he makes the key mistake of handing Hannibal Lecter over to people who don't understand how dangerous he can be, which gives Hannibal the opportunity to escape.
Paul Krendler of the same series definitely qualifies, though it only becomes noticeable in Hannibal. In many ways he's far more of a Smug Snake than Chilton was on his worst day. Like Chilton, he gets his comeuppance at the hands of Lecter.
Prince Regal in Robin Hobb's Farseer trilogy. A spoiled, petty, selfish youngest prince, he is obsessed with ruling and having power while being completely incompetent as a ruler. Like the example of Cersei above, he is much less clever than he thinks he is.
Uriah Heep in Dickens' David Copperfield is one of literature's most notable smug villains; he has the ability to make the term of address "Master Copperfield" seem insincere, and is always wittering on about how "humble" he is. Naturally, he's planning to swindle everything away from the other characters.
Mr. Collins in Pride and Prejudice, whilst not exactly a villain, is rather smug and slimy, with a rather vast (and largely unearned) self-regard that makes him believe that Elizabeth Bennet is rejecting his marriage proposal out of some feminine desire to string him along when she's rather explicitly stating that no, it's because she doesn't like him.
Duke Telrii from Elantris is an example of the "thinks he's a Magnificent Bastard" type, though he winds up little more than a pawn of the book's real Magnificent Bastard, Hrathen. King Iadon from the same book is also an example- he turns out to be a lot smarter than Telrii (and a lot smarter than he lets on), but his vision is simply too narrow to let him accomplish anything of real significance, and his misogyny stops him from realizing Sarene is a threat to him until too late.
Romance of the Three Kingdoms: Dong Zhuo and Lu Bu are obvious ones, and Cao Cao has shades of it when he's opposing the nominal protagonist, but even Liu Bei has his moments of snake-ness in the eyes of a modern audience. (But that What the Hell, Hero? reaction is probably intentional, as the author was suffering from Executive Meddling.)
Yuan Shu is probably the biggest example of the book. He declares himself the emperor with only the Imperial Seal to back up his claim, and thus alienates everybody. And his petty villainy while a member of the Coalition against Dong Zhuo, withholding food from ally Sun Jian's army to keep Sun from gaining too much glory.
Cugel the Clever, of Jack Vance's Dying Earth books, while he lives on the border between this and being an actual Magnificent Bastard, usually leans towards the Smug Snake side, being a complete sociopath, and nowhere near as clever as he imagines himself. And he's the protagonist, folks.
The Dresden Files has a lot of these, but bonus points go to Quintus "Snakeboy" Cassius, a Denarian who is not only a clear-cut example of those trope, but a literal example as well.
Simon Lovelace from The Bartimaeus Trilogy is a perfect example, though he was smarter than the average Snake.
John Mandrake also counts. Actually, most of the wizards do.
As does Bartimaeus himself. Sure, he is not stupid or inept, but no amount of intelligence or power can match the size of his ego!
It was his smug, oily certainty that infuriated her. Ray had mastered the art of speaking as if he were the only adult on the planet and everyone else was weak, stupid, or insolent. Under that brittle exterior, of course, was the narcissistic infant determined to have his own way. Neither aspect of his personality was particularly appealing.
Tom in K.A Applegate's Animorphs, or rather the second Yeerk that controls him. Marco can approach being a heroic version at times and David spends the third arc of his trilogy as one.
Ironically, all three of these characters are seen actually morphing snakes. Not too subtle, K.A.
Lord Straff Venture of Mistborn is a comparatively competent Smug Snake, being a skilled long-range Chessmaster and the most powerful nobleman in The Empire apart from its Physical God leader. At the same time, though, his arrogance, lack of skill in immediate, detailed manipulations, and the numerous petty and vile traits he shows in his interpersonal relationships keep him out of full Magnificent Bastard range.
Vizzini from The Princess Bride. Although he certainly is clever, and recognizes his weaknesses, he has a colossal ego and treats everyone, even his own henchmen, like dirt. His arrogance also prevents him from recognizing that The Man in Black would never pull his battle of wits unless he knew he would win, and that there was no sure way of guessing which cup had the poison. There's a reason he's the former Trope Namer for Out-Gambitted.
Two villains from the Forgotten Realms trilogy Counselors and Kings stand out. Lord Procopio Septus is a canny and ambitious politician, but he's shortsighted and very proud, which make it possible for him to be Out-Gambitted comparatively easily if you know what you're doing. Dhamari Exchelsor, though he puts on a friendly facade, is a treacherous and venal little man often compared to a weasel or ferret both in terms of appearance and demeanor. He's sneaky, but he's too petty to have a real Magnificent Bastard's grasp of the big picture.
Ironically Dhamari did at one point artificially turn himself into something approaching a Magnificent Bastard- upon capturing an amulet enspelled to protect it's wearer from him, he wore it himself, and was protected from himself, causing him to become much more cunning, manipulative, and successful. Once he lost it, though, it was a quick trip back to Smug Snake-hood.
Gustav Fiers, aka The Gentleman from the Spider-Man novelisations, the Sinister Six Trilogy. He certainly thinks he's a Magnificent Bastard, and looks and acts the part, being an excellent Manipulative Bastard and Chessmaster, and Man of Wealth and Taste who successfully manipulates the whole of the Sinister Six, has evaded law enforcement for years, and refers to himself as an "investor in chaos". Yet he fails to earn the audience's respect due to his contemptuous attitude and his unpleasant personality, utter heinousness (only his genuine affection for his equally monstrous brother, Karl, keeps him from being a total monster), and underestimation of Spider-Man, The Chameleon, and Dr. Octopus put him squarely in this trope.
Count Olaf of A Series of Unfortunate Events is a huge one. He has some pretty Paper Thin Disguises (to the Baudelaires, at least) and he constantly remarks about how evil and cunning he is. Also, he suffers from plot-relevant Villain Decay and he clearly lacks common sense (seeing as he asks the Baudelaires to buy some roast beef with their fortune when he knows they're not eligible yet).
Philonecron from The Cronus Chronicles. He considers himself an evil genius, and treats everyone he meets like dirt, but is defeated by two middle-school kids.
In Death: Some of the murderers are definitely this. A notable example is Dr. Waverly in Conspiracy In Death. He is so arrogant and has such a God complex that he simply assumes one of his security droids will handle Roarke easily. He clearly doesn't know Roarke at all. He happily gives the names of the people he's been working with to Eve while he's got a hostage. He had been conducting experiments on regenerating human organs, using sidewalk sleepers and poor people as guinea pigs, and the experimentation resulted in their deaths. He flies into a pompous speech about how his serum can be used on any organ, and eventually will be used on bone, muscle and tissue, which will eventually result in perfect human beings. Oh, and he'll get to decide who will be part of the survival of the fittest, and he boasts that the world will be a better place without the dregs that weigh it down. However, when Eve turns the tables on him, he gets scared, and begs for his life. Yep, he thought he was so great and smart...but he wasn't.
In general, as soon as a bad guy says something about how they're going to take down or hurt Roarke easily, you know s/he will be put in this category. The Dirty Cop Jerry Vernon from Judgment In Death is a good example. He gets in Eve's face about the fact that she is looking for dirt on him, and he brags about how he is going to sue her and bleed that rich husband of hers. No one bleeds Roarke. If s/he tried, he would squish that person like the bug s/he is.
The Idiot features Ferdyshchenko, who establishes himself as a thoroughly smug snake in one scene and doesn't do much else for the rest of the novel. At a party, Ferdyshchenko proposes a bizarre parlor game where all the participants confess the worst misdeed they ever committed. His confession was a story about stealing 25 rubles (for no reason whatsoever) from a house he was a guest at, then allowing a maid to take the blame for the theft, ultimately resulting in said maid being fired. From the way he tells his story, it's clear that he expects his listeners to be impressed with him—upon realizing that his story had exactly the opposite effect, he gets pissy and stays that way for most of the evening.
Zil Sperry from Gone, a Hitler expy whose plans are mostly either nuisances, with their only major negative effects being unintentional, or things he's tricked into doing by Caine, yet he thinks he's leading a major, important movement. When he's killed by Dekka in book 3, nobody was upset.
Stopwatch of the Whateley Universe. Brilliant planner, head of The Masterminds, has managed to hide his best power from the Superhero School Whateley Academy powers testing guys... and gets pwned by Phase in "Ayla and the Networks". He ends up having to beg Ayla for help, and loses control of his own team of supervillains.
From The Girl With The Dragon Tattoo, Nils Bjurman thinks he's being extremely clever by using his control over a mentally incompetent girl's money to coerce her into submitting to his fondness for sadistic rape and torture, especially since he thinks it unlikely her word would be believed over his if she tried to report him. However, the book explicitly makes it clear that he makes no effort to cover the physical evidence he leaves on and in her, and that if she did go to the police, mentally incompetent or not, he would be finished immediately. Also, even ignoring this mistake (and the more serious one of the girl in question being LisbethSalander,) his crimes are so heinous that there is no way he could ever incite any reaction beyond absolute disgust and contempt from the reader.
From The Girl Who Played With Fire, Alexander Zalachenko, Lisbeth's father, clearly thinks he's a Magnificent Bastard, but falls very squarely into this trope. Even though he was a competent spy for the Soviets, his arrogance and lack of self-control led him to balls up an assignment so badly that he needed to defect to save his own skin. After defecting to Sweden, he frequently got drunk, abused his girlfriend so badly she had permanent brain damage, and delighted in making his handlers bail him out of his self-inflicted trouble. Following his eventual departure from the intelligence networks, he became a sex trafficker (a business which even The Dragon thinks is too high-risk for the mediocre profit it brings), essentially because he was a misogynist who enjoyed having power over women. When confronted, everything he says boils down to Screw the Rules, I Have Connections!, and he continues to believe this, right up until his handlers get fed up with him and blow his head off, while telling him just how much contempt they have for him.
From The Girl Who Kicked The Hornets' Nest, Dr Peter Teleborian spends the book confident that his (falsified) assessment of Lisbeth Salander will be accepted without question, and is so used to being respected and admired that it genuinely throws him when someone does not fall for his charm and nod in agreement with everything he says. He has such faith that his connections will keep everything under wraps that he doesn't even do a good job of covering his tracks, and when his connections are compromised, the glaring errors become clear to everyone. However, his main flaw is that he has come to believe his own lies, and consequently completely underestimates his former patient. Also, he is a sadistic pedophile, so would be disqualified from Magnificent Bastard-dom even if he hadn't screwed everything up.
In terms of competence, the Section qualify, as they spend virtually the entire book being Out-Gambitted to the point of Epic Fail by Salander's friends while believing they have the upper hand. Also, as Cold War veterans, they are unsuited to the 2000s, and they seem unable to understand that you can no longer expect everyone in the country to tolerate your crimes simply because they were committed in the interests of "National Security", and when a younger man tries to get them to realise that times have changed, they dismiss him as lacking the spine needed to do his job.
Dr Bill Tanner from Snakehead is a disgusting scumbag who tries to sell Alex's organ's on the black market. He's so smug he brags about how Alex can't escape, which helps him break out. He's so unlikeable when he kills himself, the audience feels no sympathy.
Mr Antler from the Mediochre Q Seth Series is an example. He's almost unbearably smug, even though he actually gets successfully duped or manipulated not only by the heroes but by most of the other villains. Including Maelstrom.
Airframe: Bob Richman, who comes from the family that founded the aircraft company the book centers around. Despite that, he holds no loyalty to it, or them, and turns out to be in on a plan to allow John Marcer to cut a deal that will put him in charge of the entire company by arranging for Casey Singleton to take the fall.
In The Caine Mutiny, Lt Thomas Keefer, definitely. The attorney Barney Greenwald, to some extent.
Primate Annias in The Elenium definitely qualifies. One of the most spectacular examples of this was an attempt to frame the protagonist's fellow knights for a blasphemous massacre. Unfortunately for the plan, the Pandion Knights found out about the impending massacre first and warned the prospective victims, even turning the massacre back on the would be murderers. And unfortunately for Annias, he was relying on the massacre to take place and giving fake evidence of the Pandions' involvement before the Pandions could respond to the event. This doesn't work well for him, as it becomes very obvious to everyone involved that the crime never took place when the 'murdered' duke comes forward to give evidence of what really happened.
This event, however, becomes evidence that, at least for this situation, Annias's Smug Snake qualities were slightly subverted. Sparhawk notices that, while Annias can be clumsy, he wouldn't have been that clumsy, revealing that he was Not Himself, but acting more like how a Styric would act if they were trying to deceive someone, tipping the Pandions off to Annias's associates.
It: The eponymous monster is firmly convinced of its own superiority and views humans as nothing but mere toys and a food source. However, every time the Losers manage to get the upper hand against them, It flees. During the final showdown, in which It is grievously wounded and the Losers are bearing down on It, It considers the possibility that It is Not So Invincible After All.