Here's some good reads

Change Twilight Sparkle is not who she says she is, she doesn't really know WHAT she is... by tom117z 148,309 words · 3,169 · 150
Daughter of Magic The Disappearance of Twilight Sparkle casted a blight of sorrow amongst her friends and family. Will her half-human daughter, Aurora, and her new friends be the cure? by Moon Glow 60,048 words · 202 · 16
Undead Robot Bug Crusaders Scootaloo has a secret. So do Apple Bloom and Sweetie Belle. What happens when the truth comes out? by Banjo64 134,524 words · 2,713 · 37

These are from my top 10 bookshelf

Three Wishes: The Cutie Mark Crusaders Before They Changed The World The Crusaders learn that they aren't like other ponies. As they uncover the secrets of their origins, the trio grow closer than ever, discovering not only their unique nature, but the incredible power that comes with it as well. by Xepher 69,046 words · 1,223 · 16
I'm a loli?!? I didn't expect this in the morning..... why the hell do i have tentacles, and why are there talking ponies all over the place here? i'm just gonna try to stay home. by aterriblewriter 126,731 words · 711 · 69
A Daughter and her Dragon Spike longed for years to have a family of his own. With Twilight's help, he applies for adoption. But what is it like to be raised by royalty? by Level Dasher 199,863 words · 1,466 · 49
The Witching Hour A new pony comes to Ponyville, but she's not all that she seems. Will the town accept Midnight Storm, or will Ponyville run her out like all the rest? by Chaotic Ink 116,509 words · 2,266 · 54
Code Lyoko: EG In Canterlot High Boarding School, Twilight and her friends fight the evil XANA in a virtual world that's somehow connected to the network. by Azure Sandora 375,653 words · 315 · 21