Perhaps there is a magical artifact in the MLP world that has the power to disrupt the balance between the living and the dead. Danny Phantom senses this disturbance and travels to the MLP world. Applejack, being the responsible pony she is, gets involved. They have to go on a quest to find the artifact and keep it safe. During their journey, they face many challenges, like dealing with other ponies who don't trust Danny at first, and they also have to overcome the obstacles set by the villains who want to use the artifact for their own evil purposes.
I'm not sure of specific fanfics that combine all three, but you could start by checking out fanfiction.net or Archive of Our Own. Search for tags related to My Little Pony (mlp), Danny Phantom, and Applejack. There might be some creative crossovers there.
One idea could be that Danny and Kim have to team up to stop a new villain who has the power to manipulate time. This would put both their skills to the test as they race against the clock. Another plot could involve a ghostly artifact that Kim discovers during one of her missions, and she has to call on Danny's expertise in the supernatural to figure out what it is and how to deal with it.
One interesting fanfic concept is that Danny and Ember are forced to work together to save the Ghost Zone from a powerful, ancient evil. They must combine their powers and knowledge. Danny's scientific knowledge about the Ghost Zone and his powers, along with Ember's knowledge of the more mysterious and musical aspects of the Ghost Zone, could lead to a great adventure and a deepening of their relationship.
One idea could be that Danny and Kim have to team up to stop a new villain who has the ability to manipulate both the ghost world and the regular world. This villain could be causing chaos in both dimensions, and only by combining their unique skills can they hope to stop it.
One idea could be that Danny and the Winchester brothers team up to fight a ghost that is causing chaos in both the Ghost Zone and the human world. Maybe it's a powerful entity that has the ability to cross between dimensions easily.
One possible plot could be that Danny, through some sort of interdimensional portal accident, ends up in the Star Wars Rebels universe. He then uses his ghost powers to help the Rebels fight the Empire. Maybe his intangibility could be used to sneak past Imperial security or his ecto - blasts could be a new weapon against stormtroopers.
One idea could be a fanfic where Danny discovers a new power that has unexpected consequences. For example, he might gain the ability to time - travel and has to deal with the chaos it causes in the timeline. Another idea is a fanfic that focuses on Danny's relationships in the ghost zone. Maybe he forms an alliance with a powerful but misunderstood ghost. A third idea could be a story where Danny has to go undercover as a human in a place full of ghosts who don't know he's half - ghost.
Some Applejack fanfics might be set in an alternate universe. Maybe in a world where Applejack has to learn a new type of farming technique from a far - off land. This would not only test her adaptability but also show how she can bring new ideas back to her family's farm in Equestria.
One idea could be that Danny discovers a new ghostly power that he uses to take revenge on a group of bullies who have been tormenting his friends. He could use his intangibility in a creative way, like sneaking into their lockers and making their things disappear.
One idea could be Danny Fenton having to deal with a new ghostly enemy that can manipulate time, making his double life as Danny Phantom even more chaotic. Another could be Danny trying to balance his high school life, including exams and relationships, while also facing a ghost invasion that only he as Danny Phantom can stop. Or perhaps a story where Danny Phantom discovers a hidden power within himself that has a connection to his human side, Danny Fenton.