Well, in some 'naruto goes to alternate universe fanfiction' plots, Naruto might find himself in a world where all the ninja clans have merged into one big super - clan. He'd have to navigate the complex politics within this new structure. Also, there could be a plot where he enters an alternate universe where the Fourth Great Ninja War never happened, but there are new threats emerging that he has to face. And then there's the idea of a universe where Naruto's parents are alive, and he has to deal with a completely different family dynamic.
One interesting plot could be that in the alternate universe, Harry is sorted into Slytherin instead of Gryffindor. This would completely change his relationships and how he approaches magic. Another plot might be that Voldemort never became evil in this alternate universe, and they end up as allies. There could also be a plot where magic works completely differently, like spells are cast by thoughts alone rather than incantations.
In Naruko fanfiction, one interesting concept could be a world where Naruko has a different set of ninja skills. For example, she might master a unique form of water jutsu that no one in the original Naruto universe has seen before. Another concept could be her relationships being completely different. Maybe she forms a strong bond with characters who were antagonists in the original story, like Orochimaru, but in this alternate universe, he has a different, more positive role to play. Also, the idea of Naruko leading a different ninja team with members from different villages could make for an exciting plot.
Sasuke is often a common character. Since they have such a deep relationship in the original Naruto story, it's likely they'll interact in the alternate universe too. Kakashi could also be a common one. He was Naruto's teacher, so it makes sense for him to be around in different universes. And Sakura, as part of the original team, is also likely to interact with Naruto in these fanfictions.
In some 'naruto goes mad' fanfictions, Naruto might be driven mad by the loss of his friends. For example, if Sasuke were to die in a battle, Naruto could lose his grip on sanity. Another plot could be the result of some dark jutsu being used on him, like a genjutsu that messes with his mind. Maybe a powerful enemy targets his mental state to turn him into a weapon against the Hidden Leaf.
In some 'naruto goes blind fanfiction', an interesting plot could be Naruto having to rely on his other senses more. For example, his sense of smell and hearing become super sharp, allowing him to detect enemies and navigate in battles like a true ninja. He might also develop new jutsus that are more suitable for his blind state, like a sound - based attack that can stun opponents.
One interesting concept could be a Naruto AU where the main characters have different elemental affinities. For example, Naruto might be a water - type user instead of wind. Another concept could be a world where the Akatsuki are the heroes. They could be fighting against an oppressive regime that the Hidden Villages support. Also, a fanfic could explore a Naruto AU where the tailed beasts are free and coexist peacefully with humans from the start.
In the alternate universe, Harry could meet different versions of his friends and enemies. His relationship with them would be very different. For instance, Hermione might be a Death Eater or Ron could be a powerful dark wizard. It would be a huge shock for Harry to deal with these new identities of people he thought he knew well.
Well, you could have a Pokemon alternate universe fanfiction where the types of Pokemon are completely different. For example, instead of Fire, Water, and Grass, there could be types like Light, Dark, and Spirit. The story could revolve around a trainer who discovers this new type system and has to learn all over again how to battle and catch Pokemon. It could also be an AU where all Pokemon are sentient and can talk freely, which would change the whole dynamic of the Pokemon - trainer relationship.
One interesting concept could be if the characters had different careers. For example, instead of being in a glee club, they could be professional dancers in a big city dance troupe. Another concept might be a world where the glee club is a secret society with special powers related to music.
One idea could be an alternate universe where Sam and Dean are vampires instead of hunters. They'd have to deal with the moral implications of feeding while still trying to protect humans from other supernatural threats. Another could be a world where the angels won the apocalypse and rule over humanity with an iron fist, and Sam and Dean are part of a resistance movement. Or perhaps an AU where the supernatural world is known to the public, and Sam and Dean are like famous superheroes in that world.