One idea could be that Loki, being the mischievous character he is, finds his way into the world of Harry Potter and Supernatural. He could start causing chaos in Hogwarts by disguising himself as various characters. In the Supernatural world, he might team up with the Winchester brothers for a short time, but then double - cross them for his own amusement.
In a more complex fanfiction, the concept of different realms in all three universes could be explored. Loki, who has knowledge of different realms, could guide characters from Harry Potter and Supernatural through a journey across these realms. For example, the characters might have to find a magical artifact that exists in all three universes to stop an impending doom that threatens to destroy all their worlds. Harry Potter characters could use their spells, the Winchester brothers their hunting skills, and Loki his trickery to achieve this goal.
Perhaps a fanfiction where Loki is sent to the Harry Potter world as a form of punishment. There, he encounters a powerful magical artifact that causes the mpreg situation. The story could then revolve around how he copes with this, his relationships with the Harry Potter characters, and how they all react to this very strange event that has no precedent in either of their worlds.
A fanfiction could involve Gabriel getting involved in the fight against Voldemort. He might use his trickster abilities to outwit Voldemort and his Death Eaters. For example, he could create illusions that confuse the enemy, which would give Harry and his allies an advantage in the battle.
One idea could be that Fluttershy somehow gets transported into the Harry Potter world. Maybe she arrives at Hogwarts as a new kind of magical creature that the students have never seen before. Her gentle nature might initially cause confusion among the more rowdy students, but she could gradually make friends with the likes of Luna Lovegood, who would be intrigued by her uniqueness.
Another concept could be that Harry Potter discovers he has a connection to Magneto's mutant powers. This might happen during a strange encounter with a dark magic object that unlocks a latent power within him. He then has to learn how to control these new abilities while also dealing with the threats in his own wizarding world, and he might seek out Magneto for guidance in a secret meeting across the boundaries of their two worlds.
One idea could be a crossover where Kakashi is summoned to the Harry Potter world by a dark magic spell gone wrong. He then uses his ninja skills and Sharingan to navigate the wizarding world, perhaps even teaching some Defense Against the Dark Arts classes with his unique combat knowledge.
Maybe in a fanfiction, Harry Potter and his friends accidentally stumble upon a hidden Cybertronian relic. This relic has some sort of power that attracts Megatron. Harry and his friends then have to defend the relic from Megatron while also trying to figure out what it does and how to use it to their advantage in the fight against Voldemort.
One idea could be a crossover where Harry Potter accidentally travels to the One Piece world and meets Whitebeard. He could learn about their different forms of magic and power, and together they face a new threat that combines the dark magic from his world and the powerful pirates in the One Piece world.
One idea could be a crossover where Harry Potter accidentally ends up in the world of Ranma 1/2. Maybe he's on a magical experiment gone wrong and lands in Nerima. He could use his magic to help Ranma deal with his curse, like creating a spell to keep him from changing into a girl when splashed with cold water.
Another concept could be a crossover where the magic in the Harry Potter universe has an unexpected effect on Android 18. For example, it could start to interact with her android systems in strange ways, giving her new powers or abilities that are a combination of magic and her android technology. This would lead to a whole new set of adventures as she tries to figure out what's happening to her.
One idea could be that Gandalf somehow gets transported to the Harry Potter universe. He could become a mentor to Harry, using his vast magical knowledge and wisdom from Middle - earth. Maybe he helps Harry understand some ancient magic that even Dumbledore wasn't fully aware of.