One possible scenario in a Naruto - Kaneki fanfiction could be that Kaneki somehow ends up in the Naruto world. Maybe through a strange portal or some sort of jutsu gone wrong. He might initially struggle to adapt to the different environment and the presence of chakra. But his own unique kagune abilities could be seen as a strange new form of power in the Naruto universe.
One common theme is identity struggle. Since Kaneki is a complex character, when he's put into different universes in crossovers, he often has to re - evaluate who he is. For example, in a crossover with a superhero universe, he might question whether he can be a hero or if his ghoul nature makes him an outcast.
Power dynamics is also a common theme. Kaneki has his own set of powers as a ghoul, and the characters in Black Butler have their own abilities. Fanfictions might play around with who is more powerful in different situations or how they can use their powers together. Another theme could be the exploration of morality. Both series touch on moral grey areas, and in the crossovers, it can be interesting to see how the characters' moral compasses interact when they meet.
There's also 'Kaneki and the Avengers Crossover'. In this fanfiction, Kaneki gets thrown into the Marvel Universe. It shows his struggle to fit in and how his different nature from the regular superheroes creates both conflict and new alliances. It's full of action scenes and some deep character interactions.
One idea could be an evil Kaneki crossover with the world of 'Attack on Titan'. Kaneki's unique kagune abilities could be a new form of weapon against the Titans. He might start off as an experiment by the Marleyans similar to how he was experimented on in the original Tokyo Ghoul story. Another idea is a crossover with 'Fullmetal Alchemist'. Here, Kaneki's struggle with his inner ghoul side could be paralleled with the Elric brothers' search for the Philosopher's Stone to regain their bodies. He could be seen as a new type of chimera in this world.
Tatsumi from 'Akame ga Kill!' would be a great pair. Tatsumi is a fighter who has a strong sense of justice, and his interaction with Kaneki, who has his own moral struggles as a ghoul, could create an interesting dynamic. They could fight together against common enemies in a crossover world.
One idea could be a crossover with the world of 'Fullmetal Alchemist'. Kaneki Ken could be a chimera created by some dark alchemical experiment. His kagune could be seen as a strange alchemical creation. Another could be a crossover with 'Attack on Titan', where Kaneki joins the Survey Corps and uses his kagune to fight Titans in a unique way.
One idea could be to have Kaneki enter a parallel universe where he has to team up with a powerful centipede - like being to fight a common enemy. Maybe they are both trying to stop an evil organization that is experimenting on ghouls and creating mutant centipedes.
A crossover with "The Avengers" would also be cool. Kaneki could team up with the Avengers to fight against a common enemy that threatens both the human and ghoul worlds. His unique abilities would add an interesting element to the superhero team.
One great Tokyo Ghoul Kaneki crossover fanfiction is the one where he crosses over with the world of 'Attack on Titan'. It's really interesting to see how Kaneki's ghoul abilities interact with the Titans. The author does a great job of creating a believable scenario where the two worlds collide.