Top Favourites

All-American Girl A pony raised amongst humans finds out about her birth mother - Rarity. by Shinzakura 435,293 words · 1,121 · 151
Denuo Fortuna She was a unicorn on the run. She needed somewhere to hide, somewhere quiet and boring. The tourist pamphlet was out of date but the place sounded ideal... Ponyville by Firecaller 259,210 words · 987 · 28
Upheaval: Reckoning Sequel to Breaking Point. The barrier is no more and the Legion is on the move. What happens next? by Visiden Visidane 263,948 words · 1,818 · 50

Ordered from best to not the best, these are currently the best, and longest, stories with an overwhelming amount of darkness and pure awesomeness. Read them.

Great Reads

Diathesis A (moderately) short story about evil lurking even in the best of us. by Spike the Scribe 10,941 words · 38 · 4
Fallout Equestria: Pink Eyes Fallout Equestria side story - A young filly begins her adventure looking for her mother. by mimezinga 134,575 words · 3,344 · 80
My Little GLaDOS GLaDOS just wants to test and be alone. Why can't any of these crazy ponies understand that? by TheApexSovereign 115,636 words · 3,829 · 117

While not specifically dark or evil, these stories have caught my attention. They are worth reading, even if you don't like their genre or storyline.

Other Greats

Hard Reset Twilight gives her life to stop a changeling invasion. Repeatedly. by Eakin 36,358 words · 8,208 · 134
Fostering Intelligence Discord deals with his abusive childhood in his own unique way. by Greytercakes 9,558 words · 166 · 1
Not My Destiny Twilight refuses to accept her ancient alicorn heritage by Smayds 37,412 words · 1,697 · 61
Visionary A tale of a changeling's reformation. by Razorbeam 109,800 words · 1,960 · 55