EEating Apple Cider Doughnuts By the Fireplace on a Chilly Autumn Evening With the Apple Family
MLP: FiM
Slice of Life
Rainbow Dash likes it a lot more than she thought she would.
Rainbow Dash
Applejack
Apple Bloom
Big Mac
Granny Smith
shortskirtsandexplosions · 15k words · 456 6 · 5.9k views
EAn Orderly Transfer of Power
MLP: FiM
Comedy
Random
A history of the time Princess Twilight Sparkle got fed up and decided to overthrow Princess Celestia. Only Twilight would make an appointment to stage a coup.
Spike
Celestia
OC
Main 6
Kris Overstreet · 8.9k words · 1,293 21 · 13k views
TOffshoots and Oddities
MLP: FiM
Romance
Comedy
Slice of Life
A late night conversation between Discord and Fluttershy brings to light new information... and an explanation for one of Ponyville's biggest mysteries.
Sex
Fluttershy
Twilight
Pinkie
Discord
Semivivus · 2.3k words · 228 8 · 3.6k views
E"Like A Real Pony.”
MLP: FiM
Comedy
Slice of Life
Its been hectic, but Spike has finally settled in as Equestria's inter-species ambassador. His latest (and trickiest) meeting is with an eccentric equine hailing from Discord's dimension. She seems to want help with a personal problem.
Spike
Screwball
Casketbase77 · 3.5k words · 146 0 · 1.8k views
TA Mauderating Influence
MLP: FiM
Romance
Comedy
Maud's new beau is a real gem of a stallion.
Pinkie
King Sombra
Maud Pie
TheDriderPony · 7.4k words · 132 4 · 2.3k views
EA Personal Touch
MLP: FiM
Comedy
Slice of Life
When a pony she’s never met claims Rarity made her dress, Rarity decides to investigate.
Rarity
Coco Pommel
Sassy Saddles
Graymane Shadow · 2.3k words · 237 3 · 2k views

Lesser-Known Favourites, Part 1

A Royal Appearance Canterlot is always abuzz with gossip, but as Hearth's Warming rolls around, there's one question on everypony's minds: Whose party will the princess attend? by FanOfMostEverything 1,446 words · 226 · 2
Futility Everyone gives into hopelessness eventually. When you're the only pony left in the world, and your name isn't actually Twilight Sparkle, what is there to hope for? by FaelaArts 4,791 words · 152 · 6
A Slice of Humble Pie Igneous Pie gives his daughters a practical lesson in humily. by Bluegrass Brooke 6,446 words · 106 · 0
Frame of Reference Twilight Sparkle tries a different tactic for her art homework. by Minds Eye 3,175 words · 291 · 2
They Call Me Flightless Fury What is it like to fly? Delve into the mind of a monster and find out. by ArgonMatrix 1,049 words · 201 · 3

I can't list all of my favourites, so here are some of the lesser-known gems I've found.

Lesser-Known Favourites, Part 2

Wyrmlysan After the fall of Discord but before the rise of Nightmare Moon, Princess Luna hunts a dragon. by Chris 3,231 words · 327 · 7
Words are Louder Derpy Hooves tries to befriend a certain purple mare new to Ponyville and its social stigmas. by Ciroton 5,455 words · 171 · 0
To Bloom Without Thorns Twilight has a flower to give a very special pony. Or rather, a very special draconequus. by LickleSoxy 3,076 words · 221 · 4
Until I take your place, I am just a white space. I was nothing, but now I am you. by Super Trampoline 1,425 words · 356 · 26
Tangled Up in Blues Blues tells of the big heartbreaks and little joys of his life, and how a bluespony made it happen. by The Descendant 38,725 words · 217 · 2

(That fourth one isn't a typo, the title is " ".)

Lesser-Known Favourites, Part 3

The Sacrifice of the Knight Bolo A dying Bolo Combat Unit falls to Equestria (Crossover from Keith Laumar's Bolo universe) by Georg 3,869 words · 242 · 2
Genesis Twilight decides to push herself to the limits, and stretch the boundaries of her magic, by accomplishing the ultimate task. by JumpingShinyFrogs 11,110 words · 571 · 16