In the Sorting Algorithm of Evil
mob bosses are usually the domain of cop shows and for super heroes a Starter Villain
before true Super Villains start showing up.
Then you have these people.
Maybe they have super powers themselves, maybe they have super powered goons under their command 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.
For those unaware "made man" is a term for someone who's fully accepted as a member of the mafia. (As opposed to a common mook.)
- Kingpin is the most well known example of this trope. Nemesis to both Spider-Man and Dare Devil Kingpin is the king of the Marvel Universe's criminal underworld and has given grief to beings several time more powerful than himself.
- While the shear 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 aka 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 continuity 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 and 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.
- In the Dresden Files stories, Chicago mob boss Gentleman Johnny Marcone is actually badass enough to gain standing as a freeholding lord recognized by the Unseelie Accords.
- 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.
- In an example more obvious in retrospect Giovanni and Team Rocket from Pokémon, especially in the  where they're still active. Later foes included Eco Terrorists, a madman bent on destroying and rebuilding the universe and Team Plasma who planned to use the legendary dragon to make people give up their Pokemon. Notably Team Rocket never summoned a legendary Pokemon to do their bidding.