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.
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.
Hermione herself could be more vigilant. If she noticed any signs of danger or people acting strangely around her, she could take precautions. She could use her own intelligence and magic to create defenses. For instance, she could set up a spell that alerts her when someone with malicious intent is near, and then she could either escape or fight back.
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.
It could be the traditional villains from the original story, like the Titans or some powerful monsters. They might torture Percy to get information or just to cause chaos.
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.
It could be the traditional villains from the original story. Maybe some of the old enemies of Percy who have a vendetta against him. For example, the Titans or some rogue demigods who oppose him for power or personal reasons.
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.