Stories you should definitely read

The Code's Apprentice For a thousand years, the Code of Harmony has ruled Equestria, and the Code of Dissonance has sabotaged its works at every turn. Now the war for control over the land will come to a head, and one unicorn's decision may decide the fate of all. by Lapis-Lazuli and Stitch 149,573 words · 1,137 · 46
The Twilight Struggle As Twilight Sparkle enters her third year amongst her friends in Ponyville, she finds herself plagued with strange dreams of an unknown power whispering dark secrets to her. What is this voice, and what does it plan for the most faithful student? by Lapis-Lazuli and Stitch 55,728 words · 878 · 25
Within and Without Luna takes the Elements of Harmony on a journey in more ways than one. by Cloudy Skies 154,174 words · 1,360 · 25
Apotheosis Twilight and Luna explore a land that appears on no map by Daetrin 46,300 words · 2,750 · 45

Some more awesome stories

My Little Dashie What would you do if you found a Filly Rainbow Dash in a box? by ROBCakeran53 12,524 words · 13,391 · 820
Dark Cloud In Equestria's most desperate hour, a mysterious hooded pony offers Twilight the most powerful, but most dangerous and mind-corrupting type of magic; Dark Magic. by D5ky 95,331 words · 74 · 6
Twilight's Song As Twilight goes throughout her new life, she takes care to never forget the special ponies that helped to mold her into who she is, even with the pain that comes with the memories. One pony in particular, however, stands out among the rest. by Radiant Dawn 10,431 words · 631 · 29
The Things We Leave Behind A year after a tragic incident, Twilight Sparkle returns to Ponyville to visit her friends. by theswimminbrony 23,097 words · 1,410 · 34

Seriously, just read these

A Bluebird's Song Rainbow Dash is struggling against her own past. Is it time for her rising star to fall? by Ardensfax 205,887 words · 1,907 · 58
Rain Games Soccer season's started back up, but Rainbow Dash just can't get her head in the game. Fortunately, that's what best friends and vice captains are for... by Bookish Delight 6,075 words · 296 · 25
Otherworldly Advice Two worlds. Two friendships. However, sometimes it takes another Rainbow Dash to say what one can't. by Bookish Delight 6,380 words · 923 · 49
Sombra. Saga of Hatred Some names are respected. Some are ignored. Some are loved. There is only one name in the whole world of Equestria that became the synonym for cruelty. This name is Sombra, and this is his story. by HiddenUnderACouch 199,570 words · 218 · 10