Damage Control: Walter Declun took over Damage Control, a company that specializes in cleaning up after superhero/supervillain fights. In order to increase profits, Declun manipulated supervillains to cause as much damage as possible and gave some of them mutant growth hormone to increase their powers. This indirectly led to the Stamford incident, which in turn led to the infamous Civil War story arc.
Ghost Rider: Deathwatch is the demonic head of a major corporation which he uses as a front for his criminal organization.
Iron Man: The comic has a couple of these. One is Obadiah Stane, a literal chessmaster whose Evil Plan caused Tony Stark to develop a drinking problem, allowing Stane to buy Stark International out from under him. Justin Hammer, another one of Stark's business rivals, commonly hires supervillains to carry out acts of intimidation and sabotage against his competitors. Hammer took control of Stane International after the latter's death, and years later sold it back to Stark for one dollar (which led to Stark having to clean up all of Stane International's shady dealings). And then there was Simon Krieger, Vice President of Roxxon Energy who helped plan the murder of Stark's parents and attempted to take control of his company through a Frame-Up. Such tactics usually have Stark responding by donning the Iron Man armor to defend his own holdings.
Hammer's daughter, Justine Hammer, also becomes one when she takes over the company.
Marvel Boy: Hexus, the Living Corporation, although that happened to be an alien Hive Mind that drew its power from people's obsession with its products.
The classic Marvel Universe version is the Roxxon Energy Corporation, a corporation whose management is perfectly willing, even eager, to use any underhanded and/or criminal tactics to secure its profits. While all the superheroes are ready to fight them, Iron Man is particularly enthusiastic since their antics make his own company look bad. Their current CEO, Dario Agger, is a recurring Thor antagonist who runs the place like a nation state / religion, is working with Dark Elves so he can invade other planets for their oil, and occasionally turns into a Minotaur.
Marvel had an actual criminal organization called The Corporation at one point, although, in something of a reversal, they started as a villainous organization (Hydra) that reorganized itself along business company lines (including things such as insurance packages for its members!)
The Mighty Thor: Thor (2014) includes Dario Agger and several other supervillain CEOs, including the latest version of the Silver Samurai - a literal Corporate Samurai whose smartphone transforms into some kind of liquid metal Powered Armor.
Spider-Man's archenemy Norman Osborn has been presented as one of these since day one when he arranged for one of his scientists to be thrown in jail for embezzlement to gain access to the formula that'd make him the Green Goblin—and ever since his return, he's gotten worse.
The Kingpin is a mob boss hiding behind the mask of a legitimate businessman and owns several companies.
