Top 5 Favourites (in no particular order)

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  Methane, She Pinkie Pinkie Pie makes first contact with an alien. Her top priority: what yummy treats can she make him? by Kris Overstreet 14,264 words · 194 · 6
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  The Bridge: A Godzilla-MLP Crossover A devastating battle in the Kaiju universe transports a small group of them, heroric, villainous, and otherwise to Equestria. New bodies, new world, new society. But what happens when something even Kaiju are afraid of follows them? by Tarbtano 1,285,076 words · 2,168 · 81
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  Mare of Steel Rainbow Dash becomes Supermare by iowaforever 78,536 words · 680 · 20
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  Eclipse A recurring nightmare convinces Luna that, since her return, she has never regained her sister's complete trust. And at the forthcoming Festival of the Eclipse, she decides to make amends with a bold gesture: she removes the moon from the sky. by 8686 64,513 words · 367 · 4
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  Ponyville Noire: Tails of Two Private Eyes Daring Do is a thief trying for a second chance. Phillip Finder is a private detective with no scruples. Ponyville is a city embroiled in corruption with war on the horizon. They may be the only hope for law and order left. by Leaf Whisper 261,228 words · 251 · 10