Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

CURRENTLY PUBLISHING PHYSICAL COPIES, UNTIL THE 25th OF SEPTEMBER: http://igg.me/at/InnerGloryFinalFund

After doing some research into the history of Alicorns, Twilight finds a dead end. When she chooses to pursue it against Celestia's wishes, she finds herself entangled in a messy history that some want forgotten. An Alicorn's position comes with sacrifice. And when given power, one will always be in want of more...

A complicated explanation for the history and intricacies of the My Little Pony universe. If you're reading this, be ready for the long haul.

A rewrite, or rather, the heavily revised and actually worth reading version of The Struggle for Power, my earlier work. Think of that as an alpha build, and this as the "released-to-the-public" program.
http://www.equestriadaily.com/2011/05/story-struggle-for-power.html

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.

After failing to stop Nightmare Moon in the ancient castle of the pony sisters, Twilight Sparkle is left with a scar that will permanently change the rest of her natural born life. As Twilight recovers from her ordeal, she finds that she is left with a difficult choice. Either live her life as a lie or sacrifice her innocence to protect the ones she loves. The path before her is set and she must now walk it alone. The sands of time continues ever onward, with everyone already trapped in its muddy depths. The sun will rise and the sun will fall. Waiting for its call, Death awaits for all.

Tags, rating, and characters can change.

Art created by:
http://cuteskitty.deviantart.com (top)
http://ventious.deviantart.com (bottom)

I just put the two together

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

Officially complete!

Trouble is brewing in Equestria, and Spider-Man is summoned to save the day! However, he takes the form of a pony upon his arrival and slowly starts to lose his powers. Now as Peter Pony Parker, he must become Equestria's new hero as the Amazing Spider-Mane, but with past failures haunting his mind, will somepony be able to give him the happiness he deserves and save him from a prophecy that ends with his death?

Across Equestria and through Earth, two hearts will join together, but one may die to ensure the survival of reality...

Cover image drawn by jmkplover and colored by Saljian

Official Theme Song done by XAVI- Playful Banter

It even has a Tvtropes page!

Spiders and Magic: Rise of Spider-Mane

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.

Having lost much of her past, memories and purpose in life, Aurora Borealis stumbles upon the junkyard and its sole inhabitant Scraps. Having regained her name and desiring to find her past and place in the world, she begins to walk the paths of discovery. But what she finds and what impact she has may be more than she ever expected.

Deep in the Royal Library is a book. A terrible book that is said to send whoever reads it mad. A book so dangerous that it has to be hidden away and secured with chains to prevent it from ever being opened.

A book which has just been accidently checked out by Spike on behalf of Twilight Sparkle.

The Star In Yellow is rising once more, and only Rainbow Dash and Spike can save Twilight before it's too late. Ideas live forever. Ponies do not.

This fic is loosely inspired by the 19th century story 'The King In Yellow'.

In Equestria's far future, one thousand and five years after the return, a dysfunctional group of argumentative ponies must quest to defeat the most dangerous enemy of Equestria to ever live; the malevolent Lord Second, one of the only known members of the race of elder gods known as the humans, and the ancient cult who worships him, the Brotherhood of Man.

An over-the-top surrealist comedy, with slight serious elements. Expect a steady decline into insanity.

Cancelled, due to reasons of severe cranial trauma

Now with audio reading and prequel story, Shades of Grey, by Draven Eclipse.