Equestria Daily is a reliable source of pretty-good pony stories. But they don't like risk. For an idea of what kind of stories you're likely to find there, go look at the pony art on deviantart, and then look at the tiny subclass of it, stylistically, that ever appears on Equestria Daily. They posted Fallout: Equestria, and some other risky stories. But they have their own idea of what ponydom should be, and the pre-readers speak in their correspondence as if they had the authority to speak for EqD and for other pre-readers, so I presume they talk with each other behind the scenes about what ponyfiction should be.
At least one of the pre-readers on EqD is also a mod on fim-fiction, and you can see from the groups and blogs that pre-readers talk largely to other pre-readers. The ponyfic world is still cliquish.
For the past two months, I've been writing, and posting, roughly two thousand words a day of "Myou've Gotta be Kidding Me", a story set in a "My Little Pony: Friendship is Magic" fanfic universe, "Chess Game of the Gods". Outside of the sheer NaNoWriMo-like exercise of pushing out near-daily chapters, I've also been trying to keep in mind the various principles I've learned from Yudkowsky and LessWrong, and to try to present them in a way that people who like reading MLP fanfics might be able to appreciate.
I've just come to something of a minor climax with chapter 60, and while I'll definitely be continuing the story, this seems like a good time to mention it here, for whatever feedback and constructive criticism anyone cares to offer.