Recommended hits!

Background Pony "My name's Lyra Heartstrings, but you won't remember anything. Listen to my symphony, for it by shortskirtsandexplosions 432,377 words · 6,808 · 242
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 · 1,883 · 44
The Ballad of Echo the Diamond Dog A human finds himself in Equestria... He decides to forsake Ponyville and see the world instead. by Rust 129,595 words · 4,088 · 125
Night Guards The origins of Luna's personal guards. by Raugos 75,525 words · 1,677 · 21
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 · 940 · 68

Some of my favorites in order of most downward

Some other faves I'd suggest!

Doctor Whooves - The Series: Episode One - The Pinkie Conundrum After the harrowing events of "Traveller," the Doctor is forced into having some downtime in Ponyville while the TARDIS rests. Meanwhile, Twilight goes to confide in her beloved mentor, but ends up learning far more than she expected. by Loyal2Luna 30,783 words · 1,038 · 16
The Conversion Bureau: Last Man Standing What is there that is left for a human in a world full of ponies? by Windchaser 57,971 words · 458 · 43
The End of Ponies A lone pony of a Wasteland future Equestria finds a way to visit her dead friends in the past. by shortskirtsandexplosions 527,556 words · 1,998 · 67
The Dresden Fillies: Strange Friends Harry Dresden, Chicago's only professional wizard, accidentally travels to Equestria. What could go wrong? by psychicscubadiver 74,468 words · 2,382 · 35
Macintosh Big Macintosh seems like a simple pony who doesn't say much, but there's much more to him. by TotalOverflow 91,767 words · 193 · 5

The Wheel and the Butterfly A Dan X Pinkie Pie Saga Pinkie Pie finds herself adjusting to a new, hostile world, with a new hostile friend. Can they make it through this new misadventure together, or is it the universe that needs to watch out for them? by Justice3442 765,208 words · 2,495 · 95
Diary of a Store Clerk Living in Equestria under a false name and racial identity is one thing. Finding out you're not the only one of your kind stranded here is another... especially when that someone and the element bearers are looking for you. by GnollReader 35,047 words · 2,866 · 68
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 · 6,193 · 103
Apple of My Eye What happens when you make a wish on a falling star? well, if you're dreaming, Princess Luna might just help you out with it. And you may find yourself transformed, and living a life of romance, adventure, and craziness befitting Pinkie Pie... m by musicalreader 197,764 words · 386 · 25
Keeping It Simple Big Mac suddenly finds himself on the business end of friendship. by Ivory Piano 261,114 words · 2,185 · 42