This story is a sequel to Avocation

Life in Ponyville has been relatively quiet recently, which is somewhat surprising, given that the town's librarian tried to usurp the Equestrian throne only a few months ago. Aside from the appearance of a grumpy pegasus who set up shop as a cloudsmith, the aftermath is so unnoticeable that most ponies aren't even aware that the incident happened at all. Unfortunately, all that's about to change, thanks to the return of a certain revenge-obsessed showmare....

This is the fourth story in The Petriculture Cycle; reading the first three stories, which begin here, is highly recommended.

The artwork was provided by Page Turner, and the TV Tropes entry can be found here.

This story is a sequel to π

After Twilight Sparkle made her biggest secret public much earlier than she'd originally planned, the lives of the Element-Bearers and their closest friends somehow managed to become even more complicated than they already were. Yet despite the flurry of all of the added activity this brings, Princess Celestia decides to undertake a particularly ambitious project: the reformation of Discord. She delegates the task to Penumbra Noctis, who, more than anypony else, can empathize with the draconequus' situation, and who is therefore best suited to showing Discord the magic of friendship. On the surface, it's a very reasonable plan.

Unfortunately, Discord has never had much patience for reason.

This is the fifth and final story in The Petriculture Cycle. Reading the first four stories, which begin here, is highly recommended.

Artwork by Page Turner. TV Tropes page by an unknown number of anonymous persons on the internet.

This story is a sequel to Inscape

Penumbra seeks gainful employment. Hilarity ensues.

This is the third story in The Petriculture Cycle. The TV Tropes entry can be found here.

Artwork by Page Turner.

This story is a sequel to Petriculture

It's been several months since Pinkie Pie made a stunning admission about her past that permanently changed her relationship with her friends, particularly Twilight Sparkle, but life seems to have settled back to normal (well, normal by Pinkie Pie's standards, at least). However, when an old nemesis returns and ensnares Twilight in her influence, it's up to Pinkie to make things right.

This is the second story in The Petriculture Cycle. There is a TV Tropes Page for the entire Cycle here.

Cover image by Page Turner; "Princess Twilight" vector by Nianara.

In an effort to keep her mind occupied, Twilight Sparkle decides to delve once again into the grand mysteries of Pinkie Pie. This time, Twilight's focus is on her claims of growing up on a rock farm: like so many things related to Pinkie Pie, the idea that somepony could grow rocks as an agricultural product makes absolutely no sense. However, the investigation eventually leads Twilight to a rather... surprising discovery.

This is the first story in The Petriculture Cycle.

Artwork by Page Turner. Now with a TV Tropes page.

This story is a sequel to Rainbow Factory

Cloudsdale Weather Corporation has been running without incident for over twenty years. That is, until two foals manage to avoid being processed and find themselves in the haunted bowels of the massive facility. Can they make it out of the abandoned factory with their sanity intact? Will they uncover the secrets even a company as dark as the CWC is ashamed to keep? And what of the workers who help ensure that, in the end, not a single soul gets through...

Love the series? Buy the book!

—[TVTropes Article]—[Plagen Shiki's Reading]—[The Song Inspired by the Story]—

In the midst of autumn's splendor Twilight Sparkle, Spike, Applejack and Rainbow Dash head north to participate in the Hoftston Mare-athon segment of the annual Running of the Leaves.

Yet, as they meet the sea something seems to call Rainbow Dash down, down into the fog and uncertainty that rolls in from beyond the Everfree Forest.

What secrets of old Equestria hide in the deep woods and upon the silent shore?

*Resubmitted following revisions.*

The War of the Night, an event so hushed up that only small legends left behind tell of the time it occurred. A discovered tome, however, reveals the history of the war, of the ruling sisters, and some things best left forgotten. Some things the two ruling sisters would prefer to remain hidden...

Finally posting this from Equestria Daily, where it earned a Star 6. This is the first story in the Haven Trilogy.
http://www.equestriadaily.com/2011/06/story-solar-flare.html (Which at last count, has been Star Bombed by parasprites four times now.)

When Lance Strongshy's medical career is endangered due to relentless nightmares depriving him of sleep, his daughter Fluttershy once again overlooks the horrible past she suffered at his hooves and enlists the help of her friends to cure him. But, when the only sufficiently expedient solution turns out to be a certain spell that Twilight was instructed to never cast again, it becomes uncertain if their efforts will save him, or utterly destroy him.

A sequel to JakeHeritagu's Silent Ponyville 2, read that first if you haven't already: http://www.fimfiction.net/story/4868/Silent-Ponyville-2

And THAT one is the sequel to JakeHeritagu's Silent Ponyville so if you haven't read either here's where you should start: http://www.fimfiction.net/story/106/Silent-Ponyville

(First cover art by http://manwhomurderedtime.deviantart.com/ )
(Current cover art by http://www.fimfiction.net/user/SamRose )

The following transcripts are of a journal found in Ponyville on April 16th of this year. The last recorded contact with the town had been 3 days prior, on the 13th, when a team under orders from Princess Celestia was sent to look into several missing pony reports in the area. When another group of investigators were sent on the 16th, the town was found deserted. The journal’s owner is believed to be the princess’s personal student, Twilight Sparkle. None of the town’s inhabitants have been located in the weeks since.

Readings:
Nimbus Productions
Scribbler Productions

I highly recommend both of them.

A print version of all the stories in this series can be found here.