This story is a sequel to The Diary of Spike the Dragon

Spike is on a mission. A mission to save himself and his 'friends' from everypony. He believes that Twilight and the others are falling into their clutches and he must stop them. What happens now? Innocent lives are gone, ponies panic, and our heroes have to decide between friendship and the lives of other ponies.

War changes people and the mane six are no exceptions. In their finest hours they lost friends, family, and even themselves. Now they live their lives dealing with the stress of loss and how each of them deals with it varies from one to the other. The only thing for certain is that they've changed, they've all changed.

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

After having a mental breakdown, Scootaloo is promptly kicked out of her home and into the arms of her only supportive relative; her aunt and godmother Fluttershy. However, despite Fluttershy's expertise as a pediatrician, how she deals with Scootaloo's temperamental mental health becomes a true test of her skills as a caretaker and parent.

(Cover Art Creator: http://the-padded-room.deviantart.com )

Bioshock meets MLP in this psychological thriller, where Celestia's new faithful student, Siren Song, must discover the truth behind the city beneath the waves.

Beautiful, gifted, and faithful student of the Princess of the Sun, Siren Song has very nearly everything a pony could want. Sometimes though, in the twilight hours, Siren can see the sadness in her mentor's eyes. Once, ponies whisper, the Princess had another student named Twilight Sparkle, but she left Equestria, never to return. The pony who has a perfect life just needs one more thing—to convince Twilight Sparkle to come home so the Princess will smile again. But when Siren arrives in pursuit of Twilight, she soon finds herself trapped in a city of horrors, with only its monstrous denizens for help.

Now with a TV Tropes page!

This story is a sequel to Siren Song

Bioshock meets MLP in this psychological thriller, where Celestia's new faithful student, Siren Song, must discover the truth behind the city beneath the waves.

Since arriving in Vision, Siren has done things she never thought she was capable of—all in the name of survival. But now she abandons safety to gallop back into the darkness. Determined to do the right thing in a city gone mad, Siren must face the horrors she once fled from. But all is not as it seems in the vast and dark ocean, and Siren’s greatest foe may yet lie within herself.

Book 2 of the Vision series. Sequel to Book 1: Siren Song.

Now with a TV Tropes page!

After the events of Rainbow Rocks, Sonata Dusk find herself in a sticky situation, she doesn't have money so she gets a job at Sugarcube Corner and finds herself entangled in the life of the one girl who helped stop the Dazzling's plans.

Thank you to megatronspen ( http://www.fimfiction.net/user/MegatronsPen ) who was a big help

Every day for the past few days, a mournful song has been coming out of the alleyway beside the rescue shelter Fluttershy works at. She finally braves the scary alleyway, concerned for the possibly injured creature, but is surprised by who she has found.

Maybe, if she can show Sonata Dusk just a little bit of kindness, she can turn the poor girl's life around.

Edited by Level Dasher.

Dear Princess Twilight,
I am afraid we have made a Terrible mistake. We need your help to find a way to fix it.
Your Friend,
Sunset Shimmer.

By unknown of Celestia, when she banishes her sister to the moon, Luna is carrying a foal. But, though the foal is Luna's offspring, she cannot breath in space like her mother can. Guess how that one turns out?