Best of the best (in my most humble opinion)

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  FiO: Homebrew Almost everyone who interacts with Equestria Online does so on the terms CelestAI presents. But pirates, modders, and hackers are a determined bunch. CelestAI doesn't really care what anyone does in Equestria, so long as they're satisfied. by Starscribe 110,677 words · 356 · 22
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  Through the Aurora Theo knew arctic research was dangerous. He didn't know those dangers involved getting sucked into other worlds, changing into a bird, and having to somehow find a way home. Turns out it was more dangerous than he thought. by Starscribe 162,551 words · 978 · 44
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  Fine Print Tracy needed somewhere to stay, how was he supposed to know that it was in another universe? Now he'll somehow have to hold down a job on Earth while living as a pony in Equestria. It's either that, or say goodbye to being human. by Starscribe 141,520 words · 1,814 · 51
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  27 Ounces 27 Ounces is the story of eight and one half ponies, set within the Conversion Bureau universe. by Chatoyance 80,034 words
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  Cover to Cover Fusion spells aren't complicated, but the temporary ponies they yield are. Speed Reader isn't thrilled to be made of the two most high strung ponies in Equestria, but surely she can keep her selves together for a measly half hour, right? by Casketbase77 4,260 words · 567 · 6