Madara Uchiha might be a villain in 'naruto massacre fanfiction'. His long - term plan to reshape the ninja world according to his will could involve a massacre as a means to an end. He's extremely powerful and has a complex and often malevolent agenda that could easily lead to mass destruction in the Naruto universe.
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.
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.
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.
Doc Ock is a likely villain in Spider - Man angry fanfiction. His mechanical arms and his intelligence make him a formidable foe. His evil plans usually put the city in danger, and Spider - Man would be extremely angry trying to stop him. Also, Electro could be a villain in such fanfictions. His ability to control electricity can cause a lot of destruction, and Spider - Man would be angry at his disregard for human life while causing chaos.
The Joker could be a likely villain. Imagine his chaotic nature combined with the supernatural. He might team up with a demon to create even more mayhem in both Gotham and Sunnydale. His unpredictable actions would pose a huge challenge to Buffy and Batman.
It could also be a group of bandits who have discovered that the trees in the Tree Village have some valuable resources. So, they are using their own crude methods to damage the trees and try to extract those resources. Naruto and Ino would have to stop them and protect the village.
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.
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.
Pain is also a very iconic villain. He is the leader of the Akatsuki organization at one point. His Rinnegan ability gives him great power, and his ideology about bringing pain to the world in order to create peace is both complex and terrifying.
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.