Because I'm not allowed enough Favorites Modules to list all of my favorite stories the normal way.
And this is the narrowed down list.

First Stories of Larger Series:
Longest Night, Longest Day, by RainbowDoubleDash.
Fallout: Equestria, by Kkat.
Five Score, Divided By Four, by TwistedSpectrum.
A Dream, by totallynotabrony.
Three Wishes: The Cutie Mark Crusaders Before They Changed The World, by Xepher.
Hard Reset, by Eakin.
Trixie's Gettin' Back On Her Hooves, by Shadow Raikou.
Visionary by Razorbeam.
All-American Girl, by Shinzakura.
Like Me, by Mist.
Harmony's Wrath, by hahatimeforponies

Standalone Multi-Chapter Fics
The Dark Side, by Lord Xaos.
Her Own Pony, by Jorofarie.
Harmony Theory, by Sharaloth.
A Brief History of Equestria, by K9TheFirst1.
The End of Ponies, by shortskirtsandexplosions.
Sweetie's Mansion, by Moon Shooter.
The Sweetie Chronicles: Fragments, by Wanderer D.
Keeping It Simple, by Ivory Piano.
Clyde's Tales, by Salivanth.
Certain Advantages, by The Descendant.

One-Shots
Birds of a Feather, by AbstractThought.
Adventures in Currency Exchange: the REAL Conversion Bureau, by Elric of Melnipony
Trust, by Incredible Blunderbolt.
Rain, by FlameOfFaith.
Going Up, by Chris.
Take The Long Way Home, by Donnys Boy.
Dear Ponyville, by 1over0.
Fiddlesticks, by Tigerhorse.