The Cream of the Crop (Absolute Top Favorites)

It's a Dangerous Business, Going Out Your Door When an accident leaves Twilight Sparkle seriously ill, Applejack, Rainbow Dash, and Rarity must undertake a perilous journey to find her a cure. What adventures await them beyond Equestria's borders? by Jetfire2012 146,525 words · 1,750 · 87
A New World, a New Way To protect his Pokemon from harm Arceus has moved most of his worlds populus to Equestria in hopes that they can live in peace, but peace is often harder to obtain than one might think. by zeusdemigod131 401,927 words · 2,517 · 173
Starlight Over Detrot: A Noir Tale In the decaying metropolis of Detrot, 60 years and one war after Luna's return, Detective Hard Boiled and friends must solve the mystery behind a unicorn's death in a film noir-inspired tale of ponies, hard cider, conspiracy, and murder. by Chessie 1,460,507 words · 1,235 · 46
The Bridge: A Godzilla-MLP Crossover A devastating battle in the Kaiju universe transports a small group of them, heroric, villainous, and otherwise to Equestria. New bodies, new world, new society. But what happens when something even Kaiju are afraid of follows them? by Tarbtano 1,161,188 words · 2,069 · 80

Out of all the stories I've read, it's hard to pick just five favorites, but these five are certainly ones that have had some of the biggest impact on me, in terms of my head-canons or my community interactions.

More of my Favorites (just because)

Anthropology Lyra is determined to find out the truth behind the mysterious legends of humans. by JasonTheHuman 130,415 words · 8,358 · 170
The Path to an Empire The Crystal Empire's march cannot be stopped. Unification is its goal, and all will be brought under its flag. Leading the march is the Queen Megan herself, backed by her loyal Justiciars. With the power they wield, the enemy stands no chance. by Shocks 2,912 words · 174 · 16
Mass Effect 2 - DLC: The Equestrian Equation In this exclusive DLC, what begins as a simple search-and-rescue mission unveils a mystery millions of years in the making. Your choices are Commander Shepard's choices, and all of Equestria is at stake. by Loyal2Luna 130,318 words · 1,874 · 44
The Irony of Applejack Applejack has never told a lie. Merely... omitted some details about herself... by Mister Friendly 175,745 words · 3,418 · 81
Freeport Venture: More Equal than Others Sunset Shimmer, magus-for-hire in the corrupt city of Freeport, must track down a bank robber who dropped her loot in the middle of the poorest part of town. by Chengar Qordath 12,660 words · 826 · 23