My top favorites in no particular order

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  Earth & Sky Sequel to Windfall, set three years after. Twilight & Rarity invent artificial wings! by Warren Hutch 264,681 words · 1,212 · 28
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  The AppleDash Project A series of AppleDash scenes related to episodes. by bookplayer 32,044 words · 672 · 21
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  Into the Black: A Mare's Tale Twilight is flung into the farthest reaches of the galaxy by shirotora 149,702 words · 2,006 · 117
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  Rites of Ascension Twilight makes a new spell and starts the gears of fate with her ascension to alicornhood. (Writing started before Season 3.) by CvBrony 699,646 words · 3,079 · 79

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  Hard Reset Twilight gives her life to stop a changeling invasion. Repeatedly. by Eakin 36,358 words · 8,330 · 135
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  Unexpected Confessions Rarity and Rainbow Dash both confess their love for Fluttershy at the same time. Shenanigans ensue. by Dianwei32 218,269 words · 1,358 · 107
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  The Sword Coast With a price on Twilight Sparkle’s head and the shadow of death on her heels, her only hope for salvation is the Magic of Friendship. (Baldur’s Gate Crossover) by AdrianVesper 161,399 words · 612 · 11