Another concept could be that some of the magical creatures from Harry Potter end up in the Zelda world. Hippogriffs could be used as a form of transportation for Link and his allies. And the house - elves could have an interesting role, perhaps they help out in the various villages in the Zelda world, using their magic to clean up and cook, while also getting a taste of freedom in this new world.
One idea could be that Link, the hero from Legend of Zelda, somehow gets transported to the world of MLP. He might team up with Twilight Sparkle to fight against a common enemy that threatens both their worlds. Maybe Ganon has found a way to corrupt the magic in Equestria, and Link's combat skills along with Twilight's magic knowledge are needed to stop him.
One idea could be Link crossing over into a modern world. He'd be confused by the technology like cars and cell phones. Another could be Link teaming up with a character from another game, like Mario. They could combine their skills to defeat a common enemy.
Well, in some fanfictions, the Triforce from Legend of Zelda could be linked to the magic in Harry Potter. Maybe the power of the Triforce is seen as an ancient and extremely powerful form of magic that some wizards in the Harry Potter universe are trying to understand or control. Also, the creatures from both universes could interact. For instance, a Hippogriff might befriend a Cucco. It makes for really exciting and unique storylines.
One interesting crossover could be the use of magic spells from Harry Potter in the world of Legend of Zelda. For example, a character might use the 'Accio' spell to retrieve a key item in a Zelda dungeon. Another could be the appearance of Zelda characters in Hogwarts. Link could be a mysterious new student who has unique skills with his sword that are both magical and physical, much like some of the wizard dueling skills in Harry Potter.
Some great Legend of Zelda crossover fanfiction concepts include a crossover with the Sonic the Hedgehog series. Link could be racing through the Green Hills Zone on Epona. A crossover with the Super Mario Bros. universe is also a fun idea. Link and Mario could join forces to rescue Princess Zelda and Princess Peach from the clutches of their respective villains. Additionally, a crossover with the Kingdom Hearts series would be epic. Link could interact with Sora and the other Keyblade wielders, exploring different Disney and Zelda worlds together.
Maybe Zelda herself could be transported to the Avengers universe. With her wisdom and magic, she could assist the Avengers in different ways. She could use her magic to heal the wounded Avengers or help Tony Stark understand some ancient technology that has similarities to her own world's tech. She could also provide strategic advice based on her experience dealing with Ganon in her own realm.
One idea could be that Link, from Legend of Zelda, somehow gets transported to the Naruto universe. He might initially be mistaken for a strange shinobi with his unique green tunic and hat. Link could use his combat skills, like swordsmanship and shield defense, to team up with Naruto and his friends against common enemies, such as the Akatsuki who are after powerful artifacts. Maybe the Ocarina of Time has some sort of power that the Akatsuki wants, and Link has to protect it while in this new world.
One idea could be that Naruto and Link swap worlds. Naruto finds himself in Hyrule and has to figure out how to use the Master Sword while Link ends up in the Ninja world and tries to learn chakra control and ninjutsu. Another idea is a combined quest where characters from both universes team up to defeat a common enemy, like a powerful dark sorcerer who is causing chaos in both the Elemental Nations and Hyrule.
One idea could be that Mario and Link team up to save both the Mushroom Kingdom and Hyrule from a common enemy. Maybe a powerful dark wizard has found a way to merge the two worlds in a chaotic way, and they have to use their unique skills to restore order. Mario's jumping and power - ups combined with Link's swordsmanship and item - using abilities would make for an exciting adventure.
One interesting idea could be exploring different relationships between the characters. For example, what if Hermione had a different kind of friendship with Draco? Another could be imagining new magical creatures or spells that are unique to the fanfiction world. Also, some fanfictions might explore alternate timelines, like if Voldemort had won the first war.