Some of my favourites

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  Who Is This Lord Tirek You Speak Of? A human, after a tragic accident, ends up in the body of Lord Tirek. It all goes downhill from there. by Bucking Nonsense 64,574 words · 3,493 · 159
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  The Numbers Don't Lie An ancient magical artifact causes floating lie meters to appear above everypony's heads. This causes Twilight to reflect on honesty and friendship. Based on an idea by theworstwriter. by shortskirtsandexplosions 20,101 words · 3,675 · 58
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  First Contact is Magic A message from the stars suggests that a strange race of equine aliens are coming to Earth. In about a thousand years. by Eakin 4,461 words · 1,750 · 50
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  The Moon's Apprentice Twilight Sparkle failed her entrance exams for Celestia’s school. Worse, she is a danger to both herself and others, resulting in her magic being suppressed. Dreams crushed and now one of the weakest unicorns, a nightmare comes to her. by Forthwith 412,134 words · 3,782 · 171
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  Anthropology Lyra is determined to find out the truth behind the mysterious legends of humans. by JasonTheHuman 130,415 words · 8,490 · 175