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Self-Explanatory Titles
Self Insert Goes To Equestria
Twilight Sparkle Dates A Peach [link]
Spike Finds A Thesaurus
Twilight Sparkle Bucks Flash Sentry In The Face [link]
Daring Do And The Inconvenient Princess
Daring Do And The Overdue Book [link]
Daring Do And The Letter of Resignation
Fainting Goat in Equestria
Pony pony Pony pony pony pony Pony pony
Mary Sue vs. Meaningful Conflict
Fluttershy's 21st Birthday
Octavia and Vinyl Make A Song
Pinkie Pie teaches Sex Ed
Ponies in UFO's steal our cows.
Rainbow Dash dislikes wearing her plaid kilt.
Shining Armor's Surfing Corn Dog Apocalypse
Princess Celestia gets a carrot stuck in her nose. [link]
Twilight Sparkle wears a wig.
Nyan Cat Destroys Equestria.
Pinkie Pie Defeats Hitler
Rainbow Dash in G3 Ponyville
Sweetie Belle and Sweetie Bot
Derpy has sex with everything in the library (except Spike)
Trixie Finds a Pixie
Berry Punch's House Can Talk
Rainbow Desk And Twilight Spork Get Married
Big Mac, Small Package
Ponies Are Tiny Nuclear Reactors
Sweetie Belle is a Toaster
Rainbow Dash Loses Her Daring Do Plushie And Has A Nervous Breakdown
A Series Of Increasingly Bad Ideas
Rarity Can't Open her Front Door
Gravity is Suddenly Gone for Reasons
Pony Names Suddenly Become Anagrams. "Twirk The Pagills" Is Not Amused.
Luna Spills Glitter In Her Mane And Can't Tell It Apart From The Stars
This is the Story of How a Muffin Became an Alicorn Princess, as written by Derpy Hooves
Fluttershy is employed by a fast food restaurant
Silver Spoon and the Silver spoon

That Tickles, Your Highness!
One of Luna's forms of amusement is to go into ponies' dreams every once in a while and tickle them. But are they happy with this?

The Voice of My Cello
After dying in a horrible accident, Vinyl Scratch's ghost haunts Octavia's cello, and can only speak when the cellist plays the instrument. Octavia is very relieved to hear her friend's voice again from beyond the grave, but can't focus when Vinyl speaks to her while she's playing Concerts.

Rainbow Dash Gives Blood
Rainbow Dash steps up to help ponies in need by giving blood. Too bad she has a phobia of needles.

The Lunar Gourd [Slice of life] [Tragedy] [Comedy]
After a recent assassination attempt, Celestia tells Luna to take a guard with her on her nightly walks. Instead, Luna takes a squash. Nopony dares to ask if she can tell the difference.

Rarity Explodes
After being forced to wear a particularly ugly dress for 3 days in a row, Rarity literally explodes, demolishing half a deli store and seriously injuring 26 ponies. Twilight immediately realizes it's going to be one of those days.

A Canterlot Parody
Chrysalis attacks Canterlot with BEAM CANNONS.
Twilight and Celestia must defeat the evil queen in an EPIC LIGHTSABER DUEL.
Rainbow Dash must take out the airship's beam turrets before they GLASS THE ENTIRE CITY.
Battles will be fought. Blood will be spilled. Movies will be referenced.
CAN THE FOURTH WALL SURVIVE INTACT?
PROBABLY NOT.

Lightbulb
The sun goes out. It turns out the equestrian sun is actually a giant lightbulb, and now Celestia must go on an epic intergalactic adventure to find a replacement 5 billion watt lightbulb for her planet.

Sweetie Bot And The Department Of Licensing
Following an incident involving mislabeled sodium and an exploding toilet, Celestia orders Sweetie Bot to register herself as a lethal weapon.
Join Sweetie Bot in her harrowing fight against mountains of paperwork and underpaid government employees.

The Mane 6 Play Civilization V
In which Rainbow Dash tries to take over the world, Applejack tries to stop her, Rarity tries to enlighten it, Twilight does SCIENCE!, Pinkie Pie confuses everyone, and Fluttershy develops an unhealthy obsession with enriched uranium.

Rainbow Dash Learns How To Math
Twilight is going to help Rainbow Dash with her math homework, even though Rainbow Dash doesn't want any help, and in fact isn't even in school right now. But that won't stop Twilight!
Warning: Contains non-consensual math tutoring.

Royal Bloodline
I'm Blossom Sparkle, Princess Twilight Sparkle's daughter. I'm trying to date Rainbow Blitz, Rainbow Dash's son. This would be easier if somepony wasn't trying to assassinate us every other week.

Chasing Immortality
A noble-pony wants to be immortal. After many years of searching for artifacts, spells, and potions, it becomes clear that the only way he can achieve his goal is to ask the only immortal ponies he has knowledge of. Being an arrogant aristo-pony, he believes he can make the younger, lonelier, and more vulnerable sister fall in love with him, in order for her to give him immortality so they may be together forever.

Scootacarnation
Scootaloo gets cancer and dies. Then she gets starved to death by abusive parents. Then she gets conscripted as a child soldier and killed. Then she becomes the victim of a school shooting. What is this mysterious Scootaloo, and why does she keep getting reincarnated into really crappy situations?
[link]

Collapsing The Waveform
Twilight is dating Flash Sentry. But then, the world stops making sense. As things begin to fall apart, Twilight desperately tries to hang on to her happy ending. She just wanted to be happy. What is this mysterious force that is pulling her story apart? Who is the observer who is collapsing the waveform before she can? Is it... you?

New Ponyville
Brain uploading has been invented. Naturally, the first thing a bunch of bronies do is turn themselves into ponies and build a digital Equestria. At least, they try to - things are never quite that simple.

Help, My A.I. Thinks It's A Pony
I was trying to make a clever Twilight Sparkle chatbot to keep me company, but I underestimated just how effective my nueral net simulation was. I think it's alive.

Eternal Ponata: Horseshoepin no Yume
Dying and in a coma, Frederic Horseshoepin finds himself in a world where everypony and place is named after a musical term. (Well, except for this one gray mare with purple mane who's hanging out at Mt. Rock composing poems...)

My Little Pony: Normalcy is Relative
In an alternate Equestria, the residents of Ponyville find their buildings pretty much level with each other! The soap streets are gone, replaced with dirt! Unflavored clouds let out water instead of chocolate! Rabbits with short legs! And what happened to the customary dancing buffalo? Could all this zaniness be the work of Discord?

High Fright
You have a case of acrophobia. Therefore, it is only fitting that your entry point into Equestria be... Rainbow Dash's house. On top of that, while you like her and all, she's your least favorite of the Mane 6. Seems the cosmos has a sense of humor.

Revolt
Several background ponies are angry at Hasbro because Hasbro has given them to different names. Ponies among them include Rising Star aka Neon Lights, Bon Bon aka Sweetie Drops, and Suri Polomare aka Buttonbelle.

Rainbow Dash Invests In The Cloud
After hearing how the Cloud is going to solve everypony's problems, Rainbow Dash decides to move all her stuff to it.
Predictably, this is a terrible idea.

Girl's Night Out
At Eris’ “request”, a group of Villainesses get together for a night on the town. However, the gathering of the six big bad’s of Equestria getting together tends to draw some unwanted attention from the Elements of Harmony. Can the five Villainesses enjoy their night out with the Element wielders hot on their tails?

A Different Kind Of Sonic Boom
A young Earth pony farmmare is turned into a pegasus. Ecstatic, she starts flying all the time. (Not literally, just, y'know, even when she could just walk.) She eventually flies so fast that it causes an explosion of wheat, rye, and other things of that sort. But the fic ends before the characters can figure out a name for it. (Alternatively, they just call it a Sonic Cerealboom. I dunno, I just feel like setting up a pun and then leaving it for the readers to realize it.)