One possible villain could be a disgruntled teacher. For example, a teacher who doesn't like Hermione's know - it - all attitude. This teacher could set her up to look bad in front of the other students and faculty. Additionally, a wizard from the outside world who has a grudge against Hermione's family or friends might frame her as a way to get back at them.
It could be a jealous classmate. Maybe someone who's always in Hermione's shadow, like a fellow Gryffindor who wants more attention. They could frame her to get her out of the way. Also, there's a chance that a Death Eater sympathizer in the school could frame her as part of a larger plot to disrupt the order in Hogwarts.
It could be Orochimaru. He's always been a sneaky and devious character. He might frame Naruto to create a distraction while he tries to steal some valuable secrets from Konoha. Another likely villain could be Danzo. He has his own motives and is not above using underhanded tactics. He could frame Naruto to get rid of him as he sees Naruto as a potential threat to his power and control over the village.
Some dark wizards or witches who oppose the new order at Hogwarts after the fall of Voldemort could also be the villains. They might see Hermione as a threat to their plans of taking over or causing chaos in the wizarding world. They could force her to do things against her will in order to gain an advantage over the good side.
The Death Eaters could be likely villains. They are known for their cruel and dark ways in the Harry Potter universe. They might target Hermione because of her association with Harry Potter, who is their sworn enemy. They could see torturing Hermione as a way to get to Harry or to send a message to the Order of the Phoenix.
One likely villain could be Loki. He's always up to no good and loves to play mind games, so a card game would be right up his alley. He might be the one who lures Tony into the game.
DIO could be a likely villain. Since he has a long - standing feud with the Joestar family. He might try to take advantage of the situation where Jotaro and Jonathan meet to cause chaos and try to defeat them both.
The Joker could still be a major villain. Even with Batman as a god, the Joker might find some twisted way to challenge him. Maybe he'd try to drive Batman to use his god - like powers in a way that goes against his moral code. Ra's al Ghul could also be a villain. He might see Batman's new godhood as a perversion of the natural order and seek to destroy him.
In a 'naruto saves korra fanfiction', the villains could be a combination of different forces. There might be rogue benders who have turned to the dark side, using their bending abilities for evil purposes. These benders could be working with some mysterious outsiders who bring in new and unknown threats. Maybe there are ancient evils that have been awakened and they see Korra as a major obstacle. Naruto would then have to face these complex and dangerous foes to save Korra.
It could be Danzo. He's always been a shadowy figure with his own agenda in the Naruto series. In a massacre fanfiction, he might be behind it all to gain more control over the Hidden Leaf Village. He has no qualms about sacrificing others for his goals. Also, Kabuto could be a villain as he is a follower of Orochimaru and has his own motives for causing chaos.
The gorgons could be a likely villain. They might be lurking in the catacombs of Paris, waiting to turn Percy and Annabeth into stone. They could be after some powerful magic item that is hidden in the city.
Thanos is a likely one. Given their both having grand ambitions in the Marvel universe. In fanfiction, their meeting could be a battle of wills as they both want to be the dominant force. Loki might initially try to deceive Thanos, but Thanos is no fool and would see through Loki's tricks.