One common theme is family. Since they are sisters in the My Little Pony universe, many fanfics explore their family bond, like how they support and care for each other. Another theme is growth. Applebloom is younger and often fanfics show her learning from Applejack's experiences and wisdom.
Growth and learning are also common. Applebloom is younger, so often in fanfics applejack helps her to grow and learn new things, whether it's about farming, friendship, or dealing with challenges. Another theme could be the importance of tradition. The Apple family has a lot of traditions, and fanfics might show how applejack passes these traditions down to applebloom.
Well, 'Applebloom's Growth' is a fanfic that shows Applebloom learning from Applejack. It's really interesting to see how Applejack imparts her wisdom to her younger sister. There's also 'Applejack and Applebloom: A Day in the Orchard' which is a short but sweet story about a normal day of work for them in the orchard.
I've heard of a fanfic titled 'Lessons from Applejack'. In this one, applebloom is having trouble with her schoolwork and applejack steps in to teach her some valuable life lessons. It beautifully portrays the sisterly dynamic between them. There are also some fanfics that explore their relationship in the context of the whole Apple family. For example, 'The Apple Family Reunion' where their interactions with other family members also play a part in shaping their relationship with each other.
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.
Friendship is a very common theme. Since Applejack and Spike are from different species in the MLP world, their friendship is often explored. How they support each other, understand each other's differences and grow closer.
Another interesting fanfic could be set during a festival in Ponyville. Applejack and Spike get involved in the preparations. Spike's small - size but big - hearted nature comes in handy when they need to reach tight spaces, while Applejack uses her strength and leadership skills. Their combined efforts make the festival a huge success and their bond deepens.
Her loyalty. Applejack is often depicted as extremely loyal in fanfics, whether it's to her family or her friends. For instance, she would never abandon a friend in need.
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.