Rainbow Dash is grounded by a storm in Ponyville. She finds sanctuary within the library but Twilight Sparkle soon finds out that the storm isn't Rainbow's only problem. She's suffering from a very personal pegasus problem and Twilight has taken it upon herself to look after her friend during this delicate time.

A romance story with Twilight and Trixie, based in a world where Twilight and Trixie are a couple, and get together in secret to go on dates.

Today is astronomy day, and Luna's dragging her marefriend Twilight on a night-time flight.
On this flight, however, Twilight learns more about herself than the stars.

Coverart is by RyuRedwings on deviantArt and is used with their permission. Please check out their art as well, because they're extremely talented.
Warning: The comments will contain spoilers. Read at your own discretion!

Pincer is a changeling, a proud soldier of Queen Chrysalis. After the failed invasion of Canterlot, he finds himself trapped and at the mercy of Princess Celestia's Royal Guard. Believing that Celestia sees his species as nothing but soulless monsters, he prepares himself for the worst. The weeks crawl by, marked by an endless series of questions he will not answer for fear of endangering his friends and family at The Hive. As his nerves wear down and his interrogators learn just how ruthless he thinks they are, they have nothing to report but his belief that they will kill and destroy his kind without mercy.

Celestia steps in to prove him wrong, and what Pincer learns leaves him questioning everything he has ever known — but also gives him hope for what he'd never thought possible.

Cover art commissioned from http://www.demonkings.com.

Now with a TVTropes page.

Just when I thought I had found my home on earth, my family is moving again. I thought I was going to have to deal with it, but God had bigger plans for me. Plans that involve me finding my true home...

Anon may be the smallest standing in all of Equestria, but he is the largest when if comes to having fun. Always getting himself and ponies around him into shenanigans. Anon likes to take thing up to 11, and many of the ponies let him. Join us as we sit back and watch Anon do things that no human has done before.

This fic contains very large ponies.

A failed assault, a shamed monarch, and a spiteful sister.
The world has taken much from Chrysalis, but when her own nation is stolen from her, with her life almost following suit, she finds herself granted kindness from an unlikely source; the very ponies who she had wronged.
What kind of future can she hope to have, now that everything that she holds dear has been stripped from her?

Faith was another girl that fate was not kind to. Her friends were all victims of such circumstances as well. However, they were bound together by such pain as well, and were no longer alone. Faith could never ask for better people in her life, even with the lonely life she thought she had to lead.
However, the rollercoaster that was fate was about to take new loop. When a freaky storm completely turns their lives upside down, they find themselves in a place that no one would expect: Equestria. Now in a land where happiness is a commonplace, they will find themselves on a journey that will help them grow, make new friends, and, hopefully, find that happy ending they've always read about.

Link finished his quest, after that he just wants to relax. Twilight casts a spell to (hopefully) learn about another dimension's world. Somehow, Link winds up caught in it, forced into his beast form.

(Takes place at the end of season three)
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Twilight Princess is owned by Nintendo and MLP is property of Hasbro.

Traveling between parallel universes is impossible, especially during the process of regeneration, but the Tenth Doctor doesn't have time to question the facts. He's just been thrust through a tear in the fabric of reality, gotten a new body, and landed on a planet called Equestria. Specifically, he's landed in the worst possible place in all Equestria – somewhere that's ready to unleash a “big ol' storm of chaos”.

That's just the beginning of the Doctor's strange new lease on life: there's a whole host of mysteries to explore. Who is Derpy Hooves, the gray pegasus who understands more about him than even she knows how to explain? How does Princess Celestia already know him? And what's the truth behind the Order?

Above all, the Doctor needs to discover if this new universe can heal the wounds he suffered in the last. Only one thing is certain: there's an awful lot of running left to do.

(Warning: For those of you who haven't watched up to the Doctor Who episode 'The End of Time'... spoilers. Also, this story begins between Seasons 2 and 3 of FiM, and things start to... diverge from there.)

Side stories can be found at The Merely Mundane Tales (of a Mad-Pony in a Box).