One idea could be that Danny Phantom accidentally gets sucked into the My Little Pony world. He could use his ghost powers to help the ponies solve a mystery that's been haunting their land, like strange disappearances that are actually caused by a mischievous ghost pony. Danny would have to adapt to the colorful and friendly world of ponies while also trying to find a way back home.
Danny and Twilight Sparkle would make an interesting pair. Danny with his ghost - fighting skills and Twilight with her powerful magic. They could exchange knowledge about their different worlds and powers. Danny could learn about magic from Twilight, and Twilight could be fascinated by Danny's ghost powers.
One common theme is the exploration of different powers. Danny has his ghost powers and the ponies have their magic, so fanfictions often explore how these powers interact. Another theme is friendship. Just like in their original shows, the stories usually focus on how characters from different worlds can become friends and support each other.
One idea could be a crossover where Danny Phantom's powers are needed in Equestria to fight off some sort of dark magic. Maybe the ponies mistake his ghostly form for a new type of magical creature at first.
In Danny Phantom, Danny himself is often a popular choice. His cool powers and heroic nature make him a great addition to any crossover. In My Little Pony, Twilight Sparkle is a common character in fanfiction. She's intelligent and powerful, so she could interact well with Danny.
One great 'My Little Pony and Danny Phantom fanfiction' is 'Phantom in Equestria'. It has an interesting plot where Danny somehow gets transported to the world of My Little Pony. Another one could be 'The Ghostly Pony' which combines the unique powers of Danny with the magical world of ponies in a really creative way.
I'm not sure of specific titles off the top of my head, but you can try searching on fanfiction - specific websites. Look for ones with high ratings and lots of reviews. Usually, those are the better - quality ones.
A more complex concept could be a fusion of the two universes where the elements of the My Little Pony world, such as friendship and magic, interact with the ghostly elements of Danny Phantom's world. For example, the magic in the pony world could be used to enhance Danny's powers or to help him control his ghost side better. And Danny could introduce the ponies to new ways of thinking about things that are different from their normal, more positive and friendly world view.
In a My Little Pony - Naruto fanfiction, the art of chakra in Naruto could be compared to the magic in My Little Pony. The ponies' unique abilities, like Fluttershy's connection with animals, could be related to the special skills of Naruto characters. For instance, Naruto's ability to befriend others could be seen as similar to how the ponies make friends. A fanfiction could explore how these similarities and differences play out when the two groups meet, perhaps with some comical misunderstandings at first due to their very different cultures.
I like the idea of a Danny Phantom and Ben 10 crossover. Ben has the Omnitrix which gives him access to different alien forms, and Danny has his ghost powers. They could either be rivals at first, each thinking their powers are better, or they could quickly team up to face a threat that requires both their unique abilities. It would be a fun clash of two very different power - based universes.