Top favourites in no particular order.

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  Anthropology Lyra is determined to find out the truth behind the mysterious legends of humans. by JasonTheHuman 130,415 words · 8,480 · 175
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  Necromancy For Foals Far from Canterlot and forced to work in gem mines for cruel Diamond Dogs, a young unicorn named Bone Marrow's pursuit of his cutiemark reveals a unique talent: raising the dead. by Queen Sanguine Dreams 112,404 words · 2,720 · 36
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  Long Road to Friendship As punishment for her crimes, the Elements have cursed Sunset Shimmer to do favors for anyone who asks. Lucky her. And then there's that other Twilight Sparkle she keeps running into... by Albi 213,109 words · 3,595 · 86
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  Past Sins Can Nightmare Moon, reborn without her hate, ever escape her past? by Pen Stroke 201,810 words · 12,539 · 382
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  The Keepers of Discord Being a statue can drive you mad, yes? by Hoopy McGee 11,445 words · 6,626 · 90