Top 10 Favorites (in no particular order)

Gladiator Human in Equestria? Check. Trying to find his way home? Check. Surrounded by clueless candy-colored equines? Check. Magically soul-bonded to Twilight Sparkle using dread necromantic magic and an evil artifact? Check. by Not_A_Hat 387,426 words · 1,089 · 52
Mordane Stronghoof After an existential journey goes wrong, a man finds himself in Equestiria. With no way to return home he has no choice but to find a path in a new body. Will he discover a place to belong once again in this new land, or be forced to carve one out? by Mr Stargazer 34,740 words · 1,880 · 126
The Great Slave King King a slave of the diamond dogs, becomes a god and plots his revenge against those who wronged him. by TalonMach5 196,701 words · 951 · 67
Tales of the Oppressed Follow the journey of a young cynical man as his world is turned upside down. Without anywhere to turn, can he learn to set aside his preconceptions and learn to accept friendship for what it truly is? by Terran34 1,043,109 words · 1,382 · 157

Spiders and Magic: Rise of Spider-Mane Spider-Man is brought to Equestria for a second chance at life, but his luck may ruin his opportunity before it can truly begin. by Maximus_Reborn 351,265 words · 2,969 · 262
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 1,285,076 words · 2,168 · 81
TD the Alicorn Princess TD becomes an alicorn princess by BronyWriter 225,869 words · 2,609 · 136
Dexter's Lab: Equestria Doom and Gloom while things go Boom in . . . Equestria? by RenegadeAlias 189,259 words · 2,574 · 70
I Against I, Me Against You Twilight is teleported to Blood Gulch Canyon after meddling with a ship that crash landed in Equestria. She must enlist the help of the local red and blue soldiers to get home while unraveling a dark conspiracy linking her world to a shadowy agency. by Flynt Coal 388,211 words · 1,213 · 57

Honorable Mentions

When the Stars Align Starburst, the daughter of Princess Twilight Sparkle, meets one day a pony that is an opposite of her. by Borsuq 86,953 words · 1,012 · 78
Friendship is Grievous All welcome the latest visitor to Equestria... General Grievous? by Snake Staff 87,293 words · 1,351 · 91
Bad Mondays A particularly stubborn human is lost in Equestria and is trying his damnedest to find a way out, while surviving the surprisingly difficult rigours of life in a land filled with cute talking animals. Hilarity ensues. by Handyman 918,883 words · 2,493 · 79
Magic, and Mayhem, and... Murder? Oh my... Shawn Spencer, fake psychic detective, goes where no man has gone before. by Invictus 137,798 words · 994 · 21
Stardust Can Twilight earn the trust and friendship of people who are by nature suspicious and hostile to anything that isn't 'human'? by Arad 216,600 words · 6,288 · 104