My Top 5 (In no particular order)

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  Five Score, Divided by Four As a fan of the show, I always loved Rainbow Dash and her cutie mark, but I never wanted it to appear on my leg! Now that it has, all sorts of things are getting weird around here. I'm a guy, not a mare! Cartoon ponies aren't real... right? by TwistedSpectrum 277,593 words · 4,095 · 212
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  Upheaval: Breaking Point A desperate war, old enemies returning and past mistakes come together to alter Equestria forever. by Visiden Visidane 177,127 words · 2,146 · 49
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  My Little Pony: Friendship is Magic -- Off The Record A new pony is introduced to Equestria just before the fight with Nightmare Moon in Episode 1. Changing the entire story. by The King of Hearts 467,552 words · 1,892 · 298
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  Mordane Stronghoof After an existential journey goes wrong, a man finds himself in Equestiria. With no way to return home he has no choice but to find a path in a new body. Will he discover a place to belong once again in this new land, or be forced to carve one out? by Mr Stargazer 361,955 words · 1,826 · 125