Domestic Rock Science by Pineta. Read this or you are dumb as a box of rocks.

Little Clop of Horrors by my evil twin, Dinkeldash
The greatest action pony porno musical comedy ever written!

The Shadows of Yadith by EldritchSpires is a well told story written in the style of HP Lovecraft.

Celestia in Exclesis by Kolwynia tells the true story of Celestia and Starswirl the Bearded. Except for my story about Celestia and Starswirl the Bearded, which is the real true story...

Princess Celestia Gets Mugged by BronyWriter is ridiculous and grand.

Applejack is Full of Squirrels by shortskirtsandexplosions who hardly ever ships AppleDash.

The Best Night Ever by Capn_Chrssalid; you will read it over and over and over...

The Dysphoria Series by thedarkprep deserves a lot more attention.

The Immortal Game by AestheticB defines epic pony fantasy for me.