Makoto Isshiki in RahXephon, for whom this trope is partly named after (he's nicknamed "White Snake" because of his albinism and scheming). At first he's a typical Smug Snake, but in the second half of the story turns into a madman.
It runs in his family, judging from Babhem.
As a somewhat-literal example, Ash's Snivy from the Pokémon Black and White anime treats the teammates she's on good terms with and the jerks (like Emolga early on) with the same snooty abandon. Snivy, as a species, was presumed to have a personality like this before the series even started, hence the nickname "Smugleaf."
Enrico Maxwell from Hellsing is a massive jackass who enjoys forcing Integra Hellsing to say "please" to hand her over an important file - even when his direct superior -the Pope- ordered him to give her the file in compensation for a massive gaffe one of his men (Alexander Anderson) committed. He later becomes a full Knight Templar and tries to have his army kill all Protestants in London for the sin of not being Catholics.
In a much minor degree, the Gundam-homage successor to Maxwell, M'Quve.
Arguably, Orochimaru from Naruto. Sure, he's evil and fairly skilled, but he leaves a lot of the planning to his Enigmatic Minion. Also a literal example, what with his theme being snakes.
Gato of the Land of Waves arc loudly complains when Zabuza and his followers fail to kill Tazuna, despite them being stronger than him or any of the other men he has in his employ, and tries to kill both Zabuza and Team 7 after their battle in order to save money, showing considerable arrogance, overconfidence and disdain for his allies. Unfortunately, he doesn't count on the injured and Heel Face Turned Zabuza having enough strength and skill to kill him.
In Fullmetal Alchemist, Pride takes this trope and runs with it. He's a condescending little prick (literally) with all the ego you'd expect from the living embodiment of arrogance, and almost no redeeming qualities.
There's also Father Cornello. Quite arrogant despite being a mere puppet of the homunculi, and not impressive psychically compared to the rest of the cast, it's quite satisfying watching his scam fall apart right before his death.
Dante from the first anime is no better, being an egotistical, bodysnatching bitch who while quite intelligent, fails to earn the audience's respect or admiration, due to her selfishness, pettiness, willingness to destroy countries just so she can live a little longer, and attempts at taking over one of The Hero's two Love Interests (already a huge Woobie due to what she and her babyhad gone through).
Half the Death Note fandom sees LightYagami as a Magnificent Bastard. The other half sees him as just a high-functioning Smug Snake. Unlike many on this list, Light is very bright, but his A God Am I complex, childish Freak Outs ("he got me!"), borderline sociopathy and tendency towards kicking dogs, can and do cost him the sympathy of many, while his sheer ego, and tendency towards underestimating his opponents (and the incompetence of his own allies) can sometimes derail his plans and ultimately do get him killed. Light is incredibly smart, but his arrogance gets in the way of him giving some of his opponents as much credit as he should.
Kyousuke Higuchi the Third Kira, is a more traditional example, being arrogant without reason, none-too bright, unsympathetic and fully convinced that he is The Big Bad, despite being Light's puppet.
Gauron from Full Metal Panic!. Treating both allies and enemies with disdain? Check. Always speaking in a sarcastic tone, ending it with a smirk? Check. Loves to bug the protagonist and take advantage of his moral insecurity? Check. Overconfident that his plans will go exactly the way he wants? Check.
The novels reveal that he did know quite a bit more about what was going on than most people in Amalgam and Mithril thought, and that sort of justified his disdain for their ignorance. Also, his overall plan did go exactly the way he wanted it — he's the Death Seeker of the series, remember?
Leonard Testarossa also qualifies. While his smarts and charisma should, theoretically, allow him to avoid this trope, he's got too much of a superiority complex and kicks a few dogs too many for his own good. (Specially poor Kaname, considering how he beat her up when she and Sosuke aknowledged their feelings for each other)
Lampshaded in the later novels by Kaname herself (despite her Damsel in Distress status), who points out that sad and tragic past experiences do not give you an excuse to "play with the fates of other people, and flaunt a smile while you do it."
Yuri Killian became one of these toward the end of the first season of Kaleido Star, enacting a complicated revenge plot against Kalos Eido, his former boss, for the death of his father Aaron several years ago. While he succeeds in buying out Kaleido Stage and forcing most of its stars out (all the while taunting them about how they'll never make it big without him), attendance under Yuri's management dwindles rapidly because of people complaining the shows aren't as fun as they used to be. As a final insult, his ex-partner Layla Hamilton sees what he's done, attempts to fight back and finally gives him a hard slap to the face for assuming everything was Kalos' fault even after he learned that Aaron's death was genuinely accidental, and Kalos had been trying to make up for it ever since.
Yuri actually is one of the few Snakes who actually has a Heel-Face Turnand works hard to become The Atoner. Even if he goes too far in Leon's case...
Kazamatsuri Hayato from Gilgamesh, perhaps portrayed as a complete asshole in an attempt to make Evil Matriarch Kageyama Hiroko look more sympathetic in comparison.
Akihiko Kurata, the Mad Scientist from Digimon Savers, is incredibly manipulative, condescending, and selfish, and his habit of situating himself well out of harm's way until he's absolutely sure of success makes him even more infuriating. This is somewhat made up for by his extreme cowardice, which makes the times when things actually go against him very satisfying indeed.
Tomoe Marguerite from the anime version of Mai-Otome spends a lot of her time plotting against Arika and her friends (and eventually the whole of Garderobe Academy), attempting to bump them all off in an effort to get Shizuru to notice her. Her inability to control her pride and keep her hatred for Arika in check prevent her from succeeding with anything bigger than small-time crimes, though she still winds up as a Karma Houdini in the end, mainly due to her accomplice taking full responsibility for everything Tomoe did in the first half of the series (and nobody keeping close tabs on either of them).
The manga incarnations of Nagi in both Mai-HiME and Mai-Otome are far less Affably Evil and manipulative than his anime counterparts, though he is much more proactive in opposing the heroines, rather than plotting from the background. In both cases, he gets beaten pretty badly (twice in the former).
Nagi from the Mai-Otome manga partially subverts the trope by being the only version of Nagi in the mangas or animes to make a Heel-Face Turn and actually reveal himself to be a semi-decent human being. He actually dies in a Heroic Sacrifice defending the main hero! It is, however, only a partial subversion, because for most of the series, he was a complete ass.
Millions Knives from Trigun. Missing throughout the anime except for a few scenes, we're expected to take him seriously when we see him sitting down in a field sipping a glass of wine? Even though his Dragon had nearly mentally crippled Vash, Knives lost to him in the span of an episode!
Job Trunicht from Legend of Galactic Heroes is particularly notorious for throwing an interstellar nation under the bus for personal gain, multiple times. In an unusual example, he's actually aware of what a slimy scumbag he is:
Trunicht:Democracy isn't really all that remarkable. You can just look at me, Fleet Admiral. Someone like me can hold power and make others live and die as he likes. If that isn't a flaw of democracy, then what is?
One Piece both plays it straight and subverts it. There are plenty of Smug Snakes who rather satisfyingly get their asses handed to them by the Straw Hats, which makes them lose everything. The subversion comes from the fact that said snakes end up better off from said asskicking. Look no further than Wapol who after he was defeated by the Straw Hats and blown away from Drum island ended up starting a toy company, became a multi-millionaire, and married a model.
Some end up better off, but many do not. Kuro ended up forced to be a pirate again, the last thing in the world he wanted to be. Arlong lost his empire and was caught by the Marines. On the other hand, Eneru got exactly what he wanted (his own moon kingdom, meaning he's the only major One Piece villain who actually won,) and then there's the ones who win a little and lose a little, like Moria who lost his ship and his zombies but got to keep his position and had his defeat covered-up by the government (at least until he got told "You Have Outlived Your Usefulness" by Doflamingo. It seems that the ultimate fate of a One Piece villain is left up to fate (and the whim of Oda), and being evil is no guarantee of comeuppance.
Eneru also wanted to annihilate Skypeia, which he only managed to do partially before he got beaten down. So...3/4 victory?
Mr. 3 is probably the best example, primarily because he constantly harps about his tactics, when he's weaker than Mr. 4, chronically overconfident and cowardly, and not even as smart as Crocodile. He'd like to be a Magnificent Bastard, but he's far too arrogant and not as clever as he thinks.
Helmeppo's fate isn't particularly grating, though, due to a Heel-Face Turn (he's trying to clean up his act, and he wants to restore his family's good name... by recapturing his fugitive dad).
It also helps that he wasn't actually evil, just spoiled. It's shown that while he had no issues killing adults who defied him, he himself drew a line at killing children. That's probably why he got a Heel-Face Turn, and became Coby's most loyal friend and trusted partner in the Marines, eventually rising to a rank that's just below his father's, at Marine Headquarters (meaning that he is now stronger than his father, as officers stationed at Marine HQ (or the Grand Line in general) are stated to have strength three ranks ahead compared to those stationed at the Blue seas). Quite a bit of Character Development for a former Smug Snake.
Another example is Bellamy. He boasts a fifty-five million beri bounty to Luffy, who, at the time, had a bounty that was almost double that. While Luffy didn't know about his new bounty at the time, he still saw how much weaker Bellamy was than both he and Zoro, and thus did not bother fighting him. Then he stole from Luffy's friends. Luffy beat his ass with one unstretched punch. The bounty in itself is not very impressive, barely notable in the first half of the Grand Line, and nothing in the New World.
When Bellamy returns years later, while still a villain, he's embarrassed at what an unjustifiably-arrogant loser he was in those days. And oddly enough, he and Luffy now respect each other.
Jean Gedoo from Geneshaft has all the ego of being the valedictorian in his class (and Yugihair), with the "best genes" for leadership. Granted, he wasn't bad tactically, but he was far too obsessed with asserting and proving his worthiness, to the point that he would do very cruel things simply because he felt that someone - anyone - did not acknowledge his perfection...or simply because he was perfect and thus beyond judgment. That he had a problem with Mario Musicanova really grated.
All of the Chinese high eunuchs from Code Geass, who possess practically zero merits or skills of any kind and sell out practically everyone in their own country for their own benefit, while planning to either kill or marry off a lonely girl for exactly the same reason. Their deaths in particular are oh-so-satisfying to watch.
There's also Mao, who is played as a Smug Snake at first... until you learn what his deal is.
Jonathan Glenn from Brain Powerd probably thinks himself a Magnificent Bastard... and that's just his first failing! A combination of overconfidence, Kick the Dog moments, and the fact his manipulations never really go anywhere (plus, he later allows himself to become Baron Maximillian's pawn) gets him a place in this trope and makes him one of the most unsympathetic characters in the series.
Haruo from History's Strongest Disciple Kenichi, a fair weather friend with an ever-present arrogant smirk on his face who enjoys getting Kenichi into trouble (for example, by spreading the news of his victory over Tsukuba, which made Kenichi a target for Ragnarok). A lot of readers would like nothing better than crossing the pages of the manga and punch his teeth in...
And he actually has snake tongue!
He really is a Manipulative Bastard, and Kenichi's masters admit that he has genuine strategic talent, and eventually he does become an asset to the team (kind of). He still has no fighting skill and an ego the size of a zeppelin, but still...
As the series progresses, Haruo does start to demonstrate some honest dedication to his "minions" — even going so far as refusing to abandon them even in desperate situations and making decisions with the welfare of his group as a whole, leading even many of the masters of the series to observe that he has some very real leadership qualities. To top it off, he is slowly but surely sliding into Magnificent Bastard territory, even if his sense of style is...unique.
Mikoto from Flame of Recca. Her fight with Fuuko cements her as a true Smug Snake, starting from the usage of crocodile tears, slow poisoning (while gloating on how she likes seeing life fading away), and finally, scoring a default victory through silencing the referee (who was about to declare KO), knocking Fuuko out and won over a ten count. As Raiha coined, it's not her physical strength that makes her a Jyuushinshu, it's her slyness. Even Joker noted that he is really doubtful about how Mikoto ends up in the Jyuushinshu ranks. While still smuggy, she starts softening up when she got into a relationship with Mokuren. But that ends very pitifully for her.
Goryo of Muhyo and Roji prides himself on his tactics, even though his grasp of magical law is inferior to Muhyo's. Despite (technically) winning the contest against Muhyo, Goryo's plan to corner Ark fails miserably, forcing Muhyo to come to his aid. Goryo is also largely unlikable because his business model frequently involves Kick the Dog moments.
Kashmir from Overman King Gainer is a pompous ass who uses underhanded tricks to try to defeat the Yapan Exodus. He succeeds once making it so that a Dome that the Exodus stopped at is damaged forcing them to join the Exodus which causes distrust and hatred which is the main source of Kashmir's plans (it also backfires when several of them form a second squad under former Siberian Railroad member Adette). All other plans fails at which point Kashmir who is the worst recurring mecha pilot in the series than gets his ass kicked.
The condescending jerk Haraguchi from Genshiken. This is especially displayed in the manga, where he picks up one of the Genshiken's new comic releases, thumbs through it, and gives it back. When he could have gotten it for free.
The Gundam franchise has numerous Smug Snakes in it including:
Duke Dermail, Quinze and Chief Engineer Tsubarov of Gundam Wing; Dekim Barton from the OVA also qualifies, as do Victor Gaintz and Kratz Shelby from the novels. Suffice it to say, Gundam Wing had a higher concentration of Smug Snakes than any other Gundam series before or since.
Ribbons Almark is an interesting case of a character starting out as a straight Magnificent Bastard... but being unable to keep up with the rest of the field as the characters evolved, he began to rely almost exclusively on a supercomputer to counter everything his opponents had. Effectively, this led to his degenerating into a nasty Smug Snake towards the end, with some geniunely horrible moments (Anew Returner, anyone?).
Chigusa Tsukikage, the Big Bad during the Kyoto arc of Mahou Sensei Negima!. She acted all superior despite the fact that she's a Dirty Coward who hid behind a Human Shield (Konoka, her captive) whenever an enemy got near. In fact, when the inevitable happened and all her plans came crashing down around her in a spectacular manner, Chachazero, the Ax-CrazyPerverse Puppet of Evangeline, appeared before her and called her out for all of her cowardly actions before giving her an ignoble defeat: Scaring her so badly that she fainted. And as though emphasizing her "feels a lot more important than she actually is" nature, the three minions she hired and lorded over in the Kyoto arc (Koutarou, Tsukuyomi, and Fate) all turned out to both be stronger and a lot more plot relevant that Chigusa herself was in the grand scheme of things.
Much, much later on, Kurt Godel, Governor General of Ostia seems to be like this. Subverted as he's actually powerful enough to take on Negi, and might actually be (or not) an ally of the Big Bad. It turns out Kurt thinks he's a lot better at manipulation than he actually is, sending him right back into this trope, if only because he underestimated the Nakama's surveillance capabilities and didn't account for their informant from the future, although to be fair, he really had no possible way of knowing about that last one. As such, he pulls a Heel-Face Turn and joins Negi's group, and then he re-joins Ala Rubra.
Kurotowa in Nausicaä of the Valley of the Wind. Actor Chris Sarandon, who provided his voice in the English dub, even says he based his whole performance around the character's persistent sneer.
In Monster, most of the villains who aren't Johan or in some way redeemable. Kristof, Dr. Heinemann and Blue Sophie are the better examples.
Luppi, the replacement sixth Espada in Bleach was a Smug Snake in a big way; convinced of his indisputable superiority to his predecessor (Grimmjow), overestimating his skills in his fight with Hitsugaya, leering on Matsumoto as they fight and threatening to kill Orihime because he was injured in a diversion to cover for her abduction. Eventually, he gets killed in one shot by Grimmjow.
Eighth Espada Szayel Aporro Granz is also a Smug Snake; he considers himself an infallible genius and the "perfect being" despite the fact he only managed to get the advantage he had over Renji and Ishida by studying both of them and setting things up in advance to put the odds drastically in his favor when they fought. His arrogance takes a major blow when Mayuri Kurotsuchi reveals he completely outmaneuvered him scientifically, and Szayel to swearing, stomping, and screaming like a spoiled child when nothing is working. When he tries crossing his final and most heinous Moral Event Horizon ( forcibly impregnating Mayuri's "daughter" and liutenant, Nemu, with himself so he can come back to life, which kills her), he winds up suffering a horrific Karmic Death because he underestimated the depth of Mayuri's own preparations ( he gave Nemu a strange poison that took effect when Szayel Aporro used her to revive himself). Rather tellingly, despite Mayuri's own rampant sociopathy, Szayel disgusts him.
Big Bad Aizen himself also qualifies, despite being introduced as a Magnificent Bastard. Despite his impressive introduction, it soon becomes clear that Aizen's smooth talking and Gambit Roulette fetish are covering up his use of a godlike power as a crutch; once he truly takes the stage as Big Bad, instead of manipulating from the shadows, his Evil Plans end up getting his army killed for a fleeting to nonexistent tactical advantage, forcing him to do the job himself. This results in Yamamoto, Urahara (thrice, and once alongside Isshin and Yoruichi), and Gin all outmaneuvering him, which he only overcomes through having literal Plot Armor saving him from numerous life-ending attacks, including being disintegrated on the molecular level by The Dragon. Finally, when he's achieved his ultimate form and refuses to shut up about how powerful he is, Ichigo shows up and defeats him easily because Aizen underestimated him. As Aizen's power level increases, his ego increases even more, leading him to for no apparent reason stop using his incredibly effective powers of illusion because he thinks his sheer strength has become so great he no longer needs them.
Iwamoto and Akashi from YuYu Hakusho are what happen when you combine this with Sadist Teacher. They're always cooking up schemes to get Yusuke and Kuwabara expelled, but in the end always get thwarted by Yusuke and Mr. Takanaka.
To a greater extent, Gonzou Tarukane, the hideous crimelord who imprisoned and tortured poor Yukina. He thought he had everything under control but in truth, he never even remotely stood a chance against Sakyou's plan. Gonzou was doomed from the start because he thought the Togoru brothers were working for him when they really worked for Sakyou. The Oh Crap when he realizes he's been Out-Gambitted has this trope all over it.
Rishu in the Dark Tournament arc. He thought his match against Kuwabara was in the bag due to the manipulations (read:bribery) his sponsor carried out. Oh how wrong he was.
His boss Butajiri, responsible for said bribery, also suffers this when Younger Toguro finds out what he's been doing and tells Sakyo about it. Turns out he blamed Yusuke (and his team by proxy) for killing Tarukune and has been enjoying the beating they've been getting due to his cheating, then he's surprised when Sakyo informs him it was Toguro who killed him. Whom promptly does the same to Butajiri, with a flick of his finger causing his head to explode into Ludicrous Gibs.
There's also Dr. Ichigaki and Elder Toguro, both particularly loathsome examples. The latter gets truly wonderful comeuppance; first Younger Toguro punches him so hard he practically disintegrates, then when he shows up in the next arc (still alive and fully regenerated by his immortality), Kurama subjects him to a Fate Worse than Death.
Tenzen in Basilisk sees himself as a Magnificent Bastard but doesn't live up to it, making a number of embarrassing mistakes as well as horrifying atrocities. He gets himself killed several times over.
Unsui of the Juppon Gatana from Rurouni Kenshin. During his time in the series, Usui always seemed to have the one-up on his fellow Juppon Gatana members, and most definitely fit the smug part of the Smug Snake, more than willing to mock and belittle his foes by pointing out how he could see through them with his "Mind's Eye". His apparent reason for joining the Juppon Gatana was to be able to kill Shishio if he ever had the chance. But in his fight with Saito, he was faced with the fact that his true reason was to put up the appearance of still trying to defeat Shishio, and hiding his dishonour. Usui became even angrier when Saito pointed out that Shishio knew this and was playing him like an instrument. And then, when Usui tried to hold on to the shred of dignity he had left, Saito mopped the floor with him.
Ren Sohma from Fruits Basket. She's beautiful, sly, manipulative...and not just despicable, but in the end, very incompetent. She has to manipulate Rin to get her late husband Akira's box (and Rin then fails and is horrifyingly "punished" by its owner, Ren's much hated and abused daughter Akito), is humiliated by Shigure when he tells her he only had sex with her because she looks like an older Akito, and once her plans crumble, she's left as an Empty Shell of her former self.
Touga Kiryuuis very handsome, charming and manipulative — but ultimately, he's a horrendous Jerk Ass even to his sister Nanami, and he can't hold a candle to the realMagnificent Bastard of the series, Akio Ohtori.
Gouda of Ghost in the Shell: Stand Alone Complex is a quite intelligent man, but he has a massive inferiority complex which makes him quite a Smug Snake. He really likes to grate on people and put them down, and the protagonists get an idea of his plan fairly early on precisely because he's the kind of person that wants recognition of his cleverness.
Jose Porla, the leader of rival guild Phantom Lord. Sneeringly arrogant, condescending, self-centered and, above all, incredibly petty, thinks himself a lot smarter than he actually is and is utterly unable to keep his massive ego in check - the whole reason for his attacks on Fairy Tail and the whole mess that ensued was simply the fact that he was jealous of Fairy Tail's popularity. Despite trying to keep up an Affably Evil facade when things go his way, he quickly loses his cool and throws childish temper tantrums as soon as his plans get even slightly derailed. It is telling that, while he's obviously the strongest member of Phantom Lord, his BadassDragon Gajeel comes across as a much more credible threat. Since Jose is such a lowlife, his Villainous Breakdown cum Humiliation Conga at the hands of Makarov are a wonder to see.
From the same arc, we have MonsieurSol of Jose's Element Four, who was sure he could get the upper hand on Elfman by psychologically torturing him, first by reminding him of his dead sister Lisanna (okay, she wasn't dead, but nobody knew that...) and then by forcing him to watch as Elfman's other sister Mirajane was getting the life squeezed out of her. Oh, howwronghewas.
Goose from Baccano!. He's so incredibly arrogant that he goes so far as to say that the police would be stupid to try and stop him from murdering the senator's daughter and leaving her body on the side of the road just to scare him into releasing his boss from prison. Not only that, but he says all of this, right in front of the senator's wife and daughter. Really this (paraphrased) exchange sums it right up.
Goose: (To Mrs. Beriam) Our plan is to get Master Huey out of jail. The police would be stupid to try and stop the train and arrest us. Once we reach the city border we're going to kill your daughter and leave her body on the side of the tracks. Don't be stupid enough to offer yourself as a sacrifice. This way, Senator Beriam will have no choice but to give in to our demands. I know this isn't going to be much comfort but I'll shoot her myself
His "boss", Huey, isn't exactly innocent of this either.
Yu-Gi-Oh!: Seto Kaiba was a classic example during his time as the Big Bad. After his Heel-Face Turn he becomes a better person, but his Jerkass behaviours and unbelievable arrogance keep him as an Antiheroic take on this trope. His stepbrother, Noah Kaiba, stepfather Gozaburo Kaiba, and former business associates, The Big Five play the trope to the hilt, as do Bandit Keith Howard, Weevil Underwood, Siegfried von Schroeder, and Marik Ishtar. The latter's Superpowered Evil Side averts the trope, as he's far too psychopathic to really have an opinion of himself
Arguably the bigger Smug Snake during Kaiba's time as the Big Bad wasn't even himself—it was Mokuba. He challenges Yugi three times, each time extremely smug, despite him being nowhere near Yugi or Kaiba's skills, and prone to freaking out any time things seemed to go wrong for him. Then again, considering it's implied that he acted like that so his brother would like him again, he might be considered a sympathetic Deconstruction.
In Yu-Gi-Oh! 5Ds Jack Atlas was a lot like Kaiba at first. However, his first loss to Yusei hurt him much more than usual than such a case would for such a person, making his eventual Heel-Face Turn a very slow and painful process.
in Freezing, Ganessa Roland kicks off her first major role as a character beating the protagonist offscreen, bragging about her new status as top student even though she claims not to care, eventually goads said protagonist into fighting her again, claims she brought her near-defeat on herself which is followed be her getting a beatdown, then attempts to not take any punishment for when they both get in trouble for having an unauthorized fight (which fortunately fails). This is all from episode two, mind you.