My Little Pony: Night's Favored Child
Night's Favored Child is an My Little Pony alternate universe fic in which Nightmare Moon won against Celestia long ago and rules Equestria, which hasn't seen the sun in thousands of years.
Twilight becomes her student.
My Little Pony: Blueblood: Hero of Equestria
Blueblood: Hero of Equestria is an My Little Pony story where Prince Blueblood is forced into being an officer in a war with the Changelings.
He's selfish and cowardly and doesn't really want to fight, but he ends up doing some pretty heroic things because he's not as stupid or stubborn as the military higher-ups.
This fics has really engaging narration and does a good job of making Blueblood likeable.
My Little Pony: Friendship is Optimal
Friendship is Optimal is about Hasbro developing an MMO called Equestria Online run by an AI called CelestAI that's programmed to satisfy people's values with friendship and ponies.
It has one of the most realistic depictions of AI I've seen in fiction.
If you like this, you might like Friendship is Optimal: The Law Offices of Artemis, Stella, and Beat, which is a fanfic someone wrote based off of Friendship is Optimal.