Top Favorites

The Lunar Rebellion One hundred years after Luna’s banishment, unrest among the three pony tribes threatens to plunge Equestria into civil war. by Chengar Qordath 540,056 words · 1,044 · 48
The Life and Times of a Winning Pony Cloud Kicker has a wild life, and Blossomforth gets dragged along for the ride. by Chengar Qordath 361,449 words · 3,725 · 193
Keeping It Simple Big Mac suddenly finds himself on the business end of friendship. by Ivory Piano 261,114 words · 2,185 · 42
Night's Favoured Child With her new apprenticeship under Nightmare Moon, Empress of Equestria and Queen of the Eternal Night, the orphan filly Twilight Sparkle plunges head-first into the conspiracies, secrets and intrigues of the Empire. by Municipal Engines 151,320 words · 3,757 · 62

Some of the best stories I've read on Fimfiction. If you like a long, complex, and very well written story, then you may want to give these a shot.

Top Favorites Part Two- because five just isn't enough

Blue Angel A Blue Angels pilot is saved from a fiery crash by a most unexpected savior by V-Pony 778,421 words · 1,939 · 144
Background Pony "My name's Lyra Heartstrings, but you won't remember anything. Listen to my symphony, for it by shortskirtsandexplosions 432,377 words · 6,806 · 242
Anthropology Lyra is determined to find out the truth behind the mysterious legends of humans. by JasonTheHuman 130,415 words · 8,480 · 175
Past Sins Can Nightmare Moon, reborn without her hate, ever escape her past? by Pen Stroke 201,810 words · 12,539 · 382