Ryuuken Ishida rarely wears anything but white suits in the manga (beige in the anime), justified in that he's the director of a major urban hospital and has to be professionally dressed. He's also a very powerful Quincy and capable of kicking much ass (including curbstomping his very talented son) without even removing his jacket or loosening his tie.
Unlike most of the military-clothed Wandenreich, the Quincy that fought Captain Kyouraku wears a smart suit and coat. Their encounter left Kyouraku quite badly injured whereas he got off with barely a scratch.
Yuto Kigai, Seishiro Sakurazuka, and possibly Seiichiro Aoki from X1999.
Sir Integra Fairbrook Wingates Hellsing in Hellsing, who despite the "sir" title is also female. Alucard also has one under his Badass Longcoat. Luke Valentine wears a pristine white one for his assault on the Hellsing manor and gets only a single drop on him through his assault. Until the point he gets to Alucard, that is, and gets stomped.
Light Yagami of Death Note later falls into this after becoming a detective.
Campanella Freuling (female) from DOGS: Bullets & Carnage.
The Hückebein family from Nanoha Force are a villainous one, however. Apparently, they are good enough at murder that slaughtering an entire facility of mooks in chapter 17 didn't leave a single stain on their badass suits.
Fullmetal Alchemist: Whenever Roy Mustang is not dressed in military uniform, he wears damn fine period suits. He even wears a dress shirt under his uniform while seemingly everyone else uses more casual t-shirts or sweaters.
On the evil side, once he is released from prison in the manga and new anime, Zolf Kimblee is such a smooth criminal that he always dresses in a snazzy white zoot suit and fedora.
Pride (aka Selim Bradley) is always (when in human form) dressed in a button-up shirt, a waistcoat and dress shoes. We even see him in a suit, on one occasion, in Father's lair.
When he isn't dressing up as his sister, Johan from Monster is usually seen in a well-tailored suit (albeit sans necktie).
Valkyrie Lind of Ah! My Goddess. She's a professional badass, and she looks the part.
Soul Eater most obviously has Death the Kid, but Maka's uniform might also count, not to mention the positively Mafia-like black pinstripe suit Soul wears in his Black Bug Room with the grand piano.
Sebastian from Black Butler. Almost always dressed in a snappy tail coat, and able to end someone's existence in several different ways.
Much like Sebastian, Hayate Ayasaki of Hayate the Combat Butler is usually found dressed in a sharp butler suit. The same goes for every other butler such as Klaus, Nonahara, Himuro, and several others. All snappy dressers, all able to dish out brutal beatdowns to anything that threatens their masters/mistresses and friends. Hayate in particular even takes on a more cool, detached attitude as he casually dispatches gunmen, giant robots, and the various weirdos trying to cause him trouble.
Black Cat's Sven wears a smooth criminal-esque suit(with a red tie instead of a matching white tie), fedora included. In the anime it's never damaged and hardly changed, whereas in the manga, he's taken some articles off, to the point of no jacket, tie, or fedora; with his sleeves rolled up which was used to badass measures in a Back To Back Bad Asses moment with Train.
Train even gets in on the deal when he takes on Lugart Won(also an example).
Durarara!! has Shizuo in his bartender's outfit; looking very sharp as he hurls vending machines at Izaya and beats up punks on the streets of Ikebukuro.
Kenichi: The Mightiest Disciple: Saiga, the leader of YAMI. Very snazzy suit, easily one of the most powerful fighters in the series even after being involved in only a single battle.
Batman's foe The Penguin and his trademark tux and top hat.
And Black Mask.
Let's just say that Batman's rogue gallery's most notables have a... fondness of such sort of sophisticated outfits.
In the Claremont-era X-Men comics, Sebastian Shaw, the Black King of the Hellfire Club, always wore the height of Eighteenth-century fashion, complete with ruffled collars and sleeves. Most Hellfire high-rankers wore this style while meeting at the club (the men did— the women dressed less formally) but Shaw kept up the look all the time.
Whenever The Minutemen from One Hundred Bullets take a job, expect to see all of them wearing black suits and ties.
Deconstructed in Blue Estate. Two Italian mobsters are always seen wearing nice suits. Only to have them continually ruined by the work their jobs require (blood, termitesnote One was ordered to break into a decrepit house infested with termites., vomit...). One of them even questions why he spends half his paycheck on suits he knows will inevitably be ruined.
The Matrix. Agents are The Men in Black wearing conservative suits. Resistance fighters typically wear flashy black suits and shades, juxtaposing their drab, worn clothing in the real world.
Mahogany, played by Vinnie Jones, the silent butcher/serial killer who makes short work of New York subway passengers in The Midnight Meat Train. Despite his gruesome activities, he is always impeccably groomed and dressed; a fact emphasized when Leon, the photographer who has been following him, ultimately confronts and kills him, only to realize that he was only the procurer for a group of ancient demonic beings who, deprived of their delivery man, inform Leon of his new job, which he performs in exactly the same suit and hairdo.
Nicolas Cage's character in Snake Eyes changes from his sharkskin jacket to a suit jacket as a symbol that he's stopped messing about and is serious.
Collateral: Assassin Vincent wears a steel-gray suit and tie, but loses the tie as the situation grows out of his control. Michael Mann explains in the DVD Commentary that his look is designed to be as unremarkable as possible. So he's not just a Badass In A Nice Suit, but dressed to get away with murder.
Subverted in The Blues Brothers, where the brothers wear black suits, but it's soon revealed that those are the only clothes they own. They wear them to bed, into the sauna, etc. Unsurprisingly, they smell bad. Lampshaded in the sequel when Elwood tells his new partners why they have to dress the same way.
Jef Costello, the hitman from Jean-Pierre Melville's crime picture Le Samourai never leaves his apartment unless he's dressed in a suit, tie, rain coat, and perfectly positioned fedora. For that extra bit of class, he always puts on white gloves before a kill. Jef cares as much about his appearance as he does his alibi.
In Die Hard, Hans Gruber points out that he's wearing an expensive suit from the same tailor as the one worn by the Japanese business executive.
Agent Jay: (to Agent Kay) You know what the difference is between you and me? (Glasses Pull) I make this look good...
Justified by the titular The Tuxedo, which is in fact the ultimate spy gadget, providing its wearer with every possible skill you'd need for a spy mission, from gun assembly, to kung fu, to wicked dance moves.
Storm Shadow from G.I. Joe: The Rise of Cobra dons a spiffy white suit sans tie in the Paris segment, while James McCullen though not being a fighter does have a nice dark suit.
The entire Inception team gets into this at various stages, including Ariadne. Some particularly notable ones are Cobb, Arthur, and Saito in black tie at their first meeting, the hotel dream levels, and Arthur's famous hallway fight, in which he wears a three piece suit and removes only the jacket.
Lao Che in Temple of Doom poisons Indy while wearing a suit with a white bowtie, even.
Frank Lucas in American Gangster plays this one almost painfully straight; the one time he goes out in public (under protest) wearing a pimp coat instead of an understated business suit turns out to be his downfall.
On the side of evil, we have Nicodemus Archleone, who also has the standard attire of a suit. His one fashion deviation is that instead of a tie, he wears the noose that Judas used to hang himself with, as it grants him standard-issue invulnerability.
Also, Dresden himself, a few times. Notably, in Death Masks, when he attends a high-class auction with Susan, and in Cold Days, when he attends the birthday party that Mab threw for him.
Valor's Choice by Tanya Huff has a company of Confederation Marines having to fight a Last Stand in their dress uniforms (they were escorting a diplomatic contingent during negotiations to bring a new species into the Confederation). Fortunately for them, the Confederation military was Genre Savvy enough to equip even the dress uniforms with some armor protection.
Live Action TV
Alias: Julian Sark is a consummate professional, and he is rarely seen without a fine suit.
This trope was extremely common in American crimedramas of the 60s and 70s, particularly in representing characters from organized crime, who would never go anywhere, including an outdoor worksite, without putting on a full suit and tie. This trope could easily be called Wise Guys in Ties.
Lampshaded (unintentionally) in "The Frame," a very early episode of Mission: Impossible, where the team infiltrates a mob meeting at the boss's home and a major plot point hinges on one character getting spilled on and being sent upstairs to change into an entirely new suit, which the boss subsequently compliments him on.
Marcus Hamilton in the last season of Angel, who was more or less the Terminator with etiquette. After being told his friends were running from "a tall, well-dressed..." and then Hamilton bursting upon the scene, Angel remarked, "Wow. He really is well-dressed." The season previous, Gunn attended a fancy party, and in order to blend had to wear a suit...and then had to beat up a bunch of warrior monk-types, which he lamented would get blood on it. (It didn't, though. He's that good.)
He's does tend toward polos when not "on the clock". It's a good look for him.
In one particular episode Michael, Sam and Fiona dress in all black Armani to give similar impression to that uniforms give in the battlefield. That is, the impression that one belongs to a larger organization and of unified force. They succeed, of course. Also, they look fantastic.
Burn Notice is filmed on location in Miami, and Jeffrey Donovan is a martial arts expert who does most of his own stunts; so he really his being that badass, in that suit, in that weather.
White Collar The whole show is this - considering that Peter and Neal are very rarely not in suits when in the thick of action.
Put simply, villains from Heroes seem to love this trope. We have:
Mr. Linderman, from Season 1
Adam Monroe from Season 2 (who really pulls it off)
Arthur Petrelli from Season 3 (who doesn't). Maury Parkman, too.
Noah Bennet wore nothing but suits for Season 1, and a large chunk of Season 3.
Suits were the default clothes for Nathan in Season 1, and most of Season 3.
Sylar also attempts this in volume 3, and does about as well as Arthur.
Finally, though this may be stretching it, Danko from Volume 4 wore suit pants with his leather jacket.
Though they're all FBI agents (and all Badass), Aaron Hotchner of Criminal Minds is the only one on the team to consistently wear a suit throughout the show. He only takes off the jacket when he switches it out for a Kevlar vest. And in a handful of very early episodes, Derek Morgan played this trope before opting for more casual dress.
Zig zagged in The Sopranos ,the mobsters like to wear vulgar sportswear most of the time but they dress up according to their fancy businessmen status when the occasion requires it.
In Person of Interest, pretty much all Detective Carter needs to hear in a situation is "a guy in a nice suit" to know it is Reese's doing. The one time he was spotted in a leather jacket, she mused he must have had his suit at a dry cleaner. Eventually, the FBI, the US government and the criminal underworld slap him with the vigilante moniker of "the Man in the Suit".
Elias: Personally, I think they could've come up with a better name.
Elijah's brother, Klaus, has his turn in the season four finale. He arrives at graduation in a suit and literally his first action is to decapitate a witch by throwing a graduation cap.
Most characters in Suits, as one would suspect from the title.
Harmon Rabb, Jr. on JAG. Justified because he is a Navy officer on active duty.
24: Though usually he's seen in more street attire, Jack Bauer has had to dress up bit sometimes while on assignment (most notably when he infiltrates the Russian consulate in season 6 and during the White House invasion in season 7). Curtis Manning also wore a suit for most of season 4 where he first appeared, which coincidentally, happened to be the season he was most badass in. He typically wore combat gear in subsequent seasons.
In a blatant copy of Bond, the male agent in Data East's Secret Service pinball also wears one. He's accompanied by a female partner, who can be seen on the backglass and the playfield wearing a full-length gold dress while shooting at Soviet spies.
The Four Horsemen were always dressed to the nines when they weren't inside the ring, as they lived the life of playboy superstar athletes.
The Gman from Half-Life always wears a suit (and carries a brief case, just to add to the look), helping him stand out against the the generic scientists and security guards of the first game and then the ragtag resistance members of the second. He also remains decidedly professional (whatever his "profession" is) and calm compared to all the other characters.
Any Castlevania game where Ayami Kojima did the designs will have its lead character dressed in the very height of (somewhat) period-appropriate fashion, although special mention must be made of Alucard, both his dandyish dress from Symphony of the Night and his elegant double-breasted suit, complete with red pocket square, from the Sorrow games.
Tekken: Brothers Kazuya Mishima and Lee Chaolan tend to wear very lavish suits while fighting; Kazuya wears a dark violet suit with long, angular tails, and Lee wears a black tuxedo with a rose on the lapel and silk gloves. It makes some sense, given their father Heihachi's attire (fur-lined tiger greatcoat with white vest-pants combo). Others who dress in this manner in later games include Baek Doo San (three piece suit and hat), Feng Wei (mafia-style suit and open-collared shirt), and Anna Williams (cocktail dress).
Almost all the mobsters in The Godfather: The Game wear suits with ties and hats. The Cuneos and Barzinis stay in this trope despite using red and green respectively because they stand by dark shades. Your character initially doesn't have a suit, but you can buy several kinds of coats.
The first Gym Leaders in Pokémon Black and White are Cilan, Chili, and Cress. Since the Gym itself is based on a cafe all of the trainers, including the leaders themselves, are dressed like waiters. And they don't look half-bad, either.
Thane Krios wears what appears to be a space tuxedo. Space leather tuxedo, that is. His design process was long and hard to make him not only have the flair and confidence of an assassin, but also look intriguing to women. He even poses in his own personal idle animations.
Commander Shepard as well in his Cerberus officer uniform or the formal wear he procures from Kasumi's mission.
Likewise in Mass Effect 3 with the formal wear from Kasumi's mission or an Alliance officers uniform.
Bruce Wayne at the beginning of Batman: Arkham City. Played quite realistically, as the suit coat gets torn along the shoulder seams, demonstrating how restrictive and, well, unsuited to combat a suit can be.
Senator Steven Armstrong from Metal Gear Rising: Revengeance. He takes off the jacket before the first part of the fight, and midway through, he takes off the shirt.
Raiden is also wearing a business suit during the intro cutscene, but he tosses it away before the first battle. Thankfully, you can unlock a slightly different version of the suit (human hands vs gloved cyborg hands, normal shoes vs exposed prehensile cyborg feet) by beating the first level on Very Hard difficulty.
Formal suits are a common type of costume available to the male party members in the TalesSeries
It can be difficult to tell with the default colour scheme, but Frost◊ in Warframe seems to fit this trope and combine it with Badass Longcoat. It's easier to notice on Frost Prime◊ or by changing normal Frost's colours.
Each protagonist makes himself new clothes after acquiring enough alchemy ingredients. John gets a rather dashing teal suit, but Dave later one-ups him by making a tuxedo, complete with bowtie!
Dave has at least three outfits that could qualify for this trope, including the tuxedo.
The Midnight Crew, who live this trope with a healthy dash of noir and more than a touch of sociopathy (although in the case of Clubs Deuce, the "badass" part is ... debatable). Diamonds Droog especially has numerous back up suits.
Droog's counterpart, the Draconian Dignitary, in the Alpha universe admires Dad's clothing so much, he makes it mandatory for the population to wear it.
Same thing goes for the Felt, especially with Doc Scratch as through Ectobiology, Scratch was created with a magic Cueball and Lil' Cal, who had a green suit made for him by Kanaya.
Anonymous is often depicted as a hollow tuxedo or black business suit.
The Slender Man; at least one goon suspected he/it wasn't actually wearing a suit but had a very strangely-proportioned (and colored) body (for instance, his neck actually drooped like a vulture's, giving the appearance of a tie). This is just about the only element of him that appears in nearly all the stories.
Legend from the flash series Xin. In the second half he trades the full suit coat for a waistcoat, and when it's time to get serious he tears it off and rolls up his sleeves.
Bishop in Teenage Mutant Ninja Turtles 2003. He takes on all of the turtles, Splinter, Leatherhead, April, and Casey with nothing but a suit and a tie. Shredder needs his armor, foot army, and Karai/Hun to take on the Turtles alone. Truly a badass.
AgentSix of Generator Rex. He is officially the sixth deadliest person in the world. Where he ranks on the "best dressed" list was, sadly, never specified.
Brick in Young Justice. He is, needless to say, quite upset when the suit is ruined in battle. Do you know how much it costs to get a suit in his size?
Given that Stavros Garkos can break a table in two by merely punching it in anger, the Hurricanes should be glad he never tried to fight any of them in person.
Jack himself normally wears his trademark white kimono, but the episode where he fell in with some gangsters saw him don a very nice pinstripe suit.
Victor Veloci, the Big Bad of Dino Squad, though he more often fails than succeeds at his attempts to be badass
Any member of the military or police in their dress uniforms. In fact, it's worth pointing out that among the first things a soldier learns in basic training is how to shine boots and iron clothes.
In the US armed services, the Navy and Marines probably win this trope; Marine dress uniforms even have a full length lined cloak — that's right, they get an official superhero cape.
The Men in Black, the non-descript gents wearing a dark three-piece suit, reflective shades and ear piece, who work for the Secret Service, Special Branch or perhaps some shadowy organization that runs everything.
The Nation of Islam, particularly the paramilitary wing called the Fruit of Islam, exploits this trope. They always appear in public dressed in suits and bowties.
Gangsters during the 1920s often made a point of showing off their wealth and status by dressing very expensively (which in turn locked in this entire trope for gangsters for the next century).