Then you have these people.
Maybe they have super powers themselves, maybe they have super powered goons under their command, maybe they employ super technology, maybe they are Badass Normals that can stand up to the heroes, or maybe they're such a Magnificent Bastard that the heroes can do nothing to stop or even touch them. For whatever reason they are a major threat.
These characters are often used in more mature and darker superhero stories, since tropes related to Mafia usually fall into this, but even kids' shows sometimes have these characters.
To make this trope more flexible, works that don't involve superheroes can be examples, but still must be from stories that are similar to those, with the heroes having superpowers and supernatural abilities, or more conventional villains being also part of the cast.
- Capone Bege from One Piece. He started as a mob leader, but when he dominated the whole crime underworld of the West Blue, he got bored and decided to leave and become a pirate, but kept his mannerisms and mafia attire, and kept the same methods of going after leaders and then watch their organizations crumble without them. He also has superpowers; he ate the Castle-Castle Fruit, which turns his body into a fortress, he can shrink his henchmen and store an army inside himself, and place weapons inside him like cannons, whose cannonballs will revert into normal size after being fired. As his superpowers primarily involve transporting his henchmen and resources around and he uses guns in a world where most people are badass enough to not need them, he still retains the muggle spirit of this trope.
- DC Comics:
- While the sheer amount of corruption and organised crime in Gotham City is part of why Bruce Wayne became Batman, most of the mob families fall aside as Batman takes down their rings and more dangerous villains like The Joker or Poison Ivy take their place. One exception is Oswald Cobblepot, a.k.a. The Penguin, who with nothing more than connections, goons and some fancy umbrellas stands as one of Batman's major villains. The Joker himself may count depending on the adaptation. Black Mask is a modern variation.
- In Superman, Intergang is a mafia-like element in Metropolis which is a constant thorn in Superman's side. In the comics and the animated series it turns out they're supplied by Darkseid, but in Lois & Clark where there is no Darkseid it's played more straightly.
- In Kick-Ass the Big Bad is the head of the local mob: John Genovese in the comic, Frank D'Amico in the film. His son, Red Mist goes on to be the World's first Supervillain.
- Marvel Comics:
- The Kingpin is the most well known example of this trope. Nemesis to both Spider-Man and Daredevil, Kingpin is the king of the Marvel Universe's criminal underworld and has given grief to beings several time more powerful than himself. Officially he is just a normal human, but he is inhumanly strong thanks to training, and while stories show him using super techonology like his cane with a deadly desintegrator beam, he relied less on them over the years.
- There is also Tombstone, Hammerhead, Silvermane, and Count Nefaria. Most of those villains have fought the likes of Daredevil and Spider-Man but Neferia was powerful enough to take on The Avengers.
- The Hood was an Unlucky Everydude who got magical cape and shoes from certain demon that granted supernatural powers, and with that in hand he fights to became a mob boss, becoming a real menace for groups as the New Avengers. But even without his magical clothes, he's also a Badass Normal who can fight with his guns and fists.
- Joe Fixit, the original Grey Hulk alternate persona, worked as a bodyguard for the mob in Las Vegas.
- The Punisher: Once a handsome mobster Billy Russo, when his attempt to assassinate everyone connected to the Castle family almost succeeded, got thrown through a glass window by Frank, reducing his face to a scarred mess. Going crazy after that, he adopted the nickname of Jigsaw and became a formidable enemy of the Punisher; he's also tangled with Spiderman and Nightcrawler.
- Johnny Royale leads a gang with various super powered members. Johnny himself also has powers, specifically with teleportation, which doesn't seem very impressive for the leader of a superpowered gang, but comes in handy when it comes to pulling heists or establishing an alibi.
- Another case explored and deconstructed what happens when a non-powered mob boss has an underling with super powers; said underling soon becomes the Dragon-in-Chief and leaves the "boss" as an Authority in Name Only.
- The main antagonist of Shi is a Yakuza crime lord who killed her father and brother when she was a child. Being trained by a decade for her grandfather, Shi goes for a Roaring Rampage of Revenge against him, but he's also a lethal martial artist who killed a lot of people apart of Shi's family and having a tough Final Battle where she almost died, but finally could defeat him, barely.
- In Stormwatch PHD, one of the team's first opponents is the Walking Ghost, an intangible Russian mob boss who also happens to be Gorgeous' ex.
- Black Blade: Victor Draconi is the head of the Draconi family household and the Big Bad of the trilogy. Victor lives in the magical and mob-controlled city of Cloudburst Falls and has abilities and powers of his own which he steals by torturing and killing his enemies. His ultimate plan being a purge of the other crime families in control of the city to allow him to take control.
- In The Dresden Files, Chicago mob boss Gentleman Johnny Marcone is actually badass enough to gain standing as a freeholding lord recognized by the Unseelie Accords. While a completely ordinary human himself, he is fully aware of the supernatural community and regularly deals with major players like Queen Mab and Donnar Vadderung.
- Luke Cage (2016): Bushmaster in season 2. Head of the Brooklyn-based Stylers, he gains superstrength from Hollywood Voodoo, is a whole other ballgame from terrorizing normal human street gangs and local crime syndicates.
- The Defenders (2017): The Hand are depicted as a syndicate of three men (Bakuto, Murakami and Sowande) and two women (Alexandra and Madame Gao) who have stayed alive for centuries thanks to resurrection substance.
- Daredevil (2015):
- Even though he's of more normal proportions than he is in the comics, Wilson Fisk still fits this trope. He's even able to break Dex's back while Dex is in the very Daredevil costume Fisk procured for him.
- Nobu in seasons 1 and 2 is introduced as an associate partner of Wilson Fisk's, but turns out to be part of the Hand and has been using the same resurrection substance as the leaders, allowing him to survive Matt setting him on fire.
- The Chairman from Sentinels of the Multiverse is this, being an expy of the likes of Kingpin and Ras. His villain deck is actually one of the harder ones to beat, even with a full hero team. The fluff even points out he has access to a Lazarus pool that keeps him in his physical prime despite being well over 100 years old.
- Inverted in ChampionsOnline with the Gemini Gang. Their leader Mr. Gemini is a supervillain with self duplication powers who figured out how use his powers to make clones of other people (though the clones get progressively weaker the less they resemble him) and decided that it would put him at a disadvantage if people found out he could do that, so he pretends he's a leader of a Gang of Hats with the theme of "the more you look like the boss, the higher your position in the gang" to hide it.
- The Elder Scrolls: In Skyrim, the main villain of the Thieves' Guild questline is the medieval fantasy version of this. The player character is, for all intents and purposes, a Physical God who, when properly leveled, takes down armies, dragons, and daedra with terrifying ease. Mercer Frey is the leader of the Thieves' Guild and at first seems to be just an unusually skilled locksmith and fighter. But it turns out he's got powers granted by the Daedric Prince Nocturnal, as well as her artifact, a magical key that can open anything. Later, the Dragonborn can acquire the same powers.
- Geese Howard from Fatal Fury series is a crime boss who has the control of the city of Southtown since The '70s during the events of Art of Fighting. But also, he was trained in the martial art of Aikido so he can beat up enemies who challenge him without help.
- Don Corneo from Final Fantasy VII, a mob leader who fits more the stereotype of bald, short, cowardly and perverted, he was in cahoots with Shinra Company, the de-facto rulers of the world, and Shinra eventually turns against him when he reveals important information to the heroes.
- In Freedom Force, one of the most annoying foes is Pinstripe, the mob boss that has the ability to control his own density, as you don't have the characters to handle him when he shows up, and his attacks are surprisingly powerful. While not immensely powerful, he is responsible for the origins of three different characters, the appearance of another, gets two separate arcs to his name, and comes directly after the threat of World War III with the Soviets.
- The Mafia of Cooks from A Hat in Time, while they are the villains from the first level, they are still a major threat for the heroine Hat Kid, while all the mafia goons are very dumb, incompetent, have terrible grammar and are terrible cooks despite their name, they are strong and can take a lot of damage without dying, their leader is much smarter and is even more strong and durable.
- Junya Kaneshiro from Persona 5 counts in a unique way. Despite being the third major boss fight and the whole reason Makoto joins the team, as well as having multiple other students under his wraps, he would certainly qualify... except you don't fight him but his Super-Powered Evil Side in the cognitive world.
- In an example more obvious in retrospect, Giovanni and Team Rocket from Pokémon, especially in the anime where they're still active. Pokémon Red and Blue, Pokémon Gold and Silver, and their remakes have them operate a lot like a Yakuza, among other things using the Viridian City Pokemon Gym as a front. Later foes included Eco Terrorists, a madman bent on destroying and rebuilding the universe, Team Plasma who planned to use the legendary dragon to make people give up their Pokemon (then later try to freeze the world to death), a cult bent on a holocaust, and an abusive mother who wants to open dimensional rifts despite the dangers. Notably Team Rocket never summoned a legendary Pokemon to do their bidding.
- Mr. X in the Streets of Rage series definitely has elements of one, especially in Streets of Rage 3 where he's revealed to have become a Brain in a Jar piloting a robot body.
- Goro Majima and Kazuma Kiryu from Yakuza count in Project X Zone 2. Being high ranking Yakuza able to stand toe-to-toe with the likes of M Bison from Street Fighter and Selvaria Bles from Valkyria Chronicles among others.
- Mobster Kingpin, the Big Bad of Problem Sleuth. He's a mob leader with access to powers and video game-like techniques just like the main three heroes. Exaggerated when his imaginary self descends in to demonhood and becomes Demonhead Mobster Kingpin, a being capable of ripping the universe in half.
- In Batman: The Animated Series, Rupert Thorne is a non-costumed, non-powered mob boss who, purely through his cunning and ruthlessness, manages to remain a major power in the Gotham underworld even among all the costumed villains. He has appeared in some other continuities, but is never as dominant as he is in the B:TAS one.