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Project: Sunflower As the Earth is under threat, humanity reaches out for one last hope of salvation. by Hoopy McGee 243,094 words · 5,164 · 92
ARTICLE 2 An alien crash lands in Equestria. It calls itself human. by Muppetz 228,756 words · 5,174 · 177
Arrow 18 Mission Logs: Lone Ranger A mission to investigate a far off world takes an interesting twist. by AdmiralTigerclaw 66,018 words · 6,219 · 88
Anthropology Lyra is determined to find out the truth behind the mysterious legends of humans. by JasonTheHuman 130,415 words · 8,482 · 175
A Twilight Landing A strange girl has shown up in another strange girl's garage. Together, can they figure out just what is going on? Will they be able to get the strange girl claiming to be Twilight Sparkle home? by MerlosTheMad 247,193 words · 1,265 · 37

If there was a sixth slot, I'd probably put Five Score, Divided by Four there.

Numbers 1, 3, and 5 correspond with the stories above them

Project Sunflower: Harmony After the events of Project: Sunflower, Erin returns to Ponyville to study magic. Meanwhile, something is stirring on the newly-discovered world of Harmony. by Hoopy McGee 171,076 words · 2,580 · 56
The Maretian Mark Watney is stranded- the only human on Mars. But he's not alone- five astronauts from a magical kingdom are shipwrecked with him. by Kris Overstreet 479,824 words · 2,459 · 49
Arrow 18 Mission Logs: Sparkle's Notes Companion Text to Arrow 18 Mission Logs: Lone Ranger by AdmiralTigerclaw 14,955 words · 2,832 · 43
Five Score, Divided by Four As a fan of the show, I always loved Rainbow Dash and her cutie mark, but I never wanted it to appear on my leg! Now that it has, all sorts of things are getting weird around here. I'm a guy, not a mare! Cartoon ponies aren't real... right? by TwistedSpectrum 277,593 words · 4,091 · 212
My Little Marriage : Mary is a Mare Stan has been married to his wife, Mary, for nearly fifteen years. They're happy and live a very normal, almost picturesque life. Sometimes... life has a funny way of pulling a one eighty when you least expect it. by MerlosTheMad 216,808 words · 1,690 · 87

Oh hey, more slots.

More favorites

Sunflower - Side Projects A collection of short stories related to Project: Sunflower by Hoopy McGee 80,900 words · 1,824 · 28
The Nemesis Starlight and Trixie have a debate concerning their relationship to Twilight by James Pwyll 2,054 words · 191 · 5
Unchanging Love With the advent of the Canterlot wedding, change is coming. Sweet Leaf is an undercover changeling love collector, wife, and co-owner to the Sweet Roast Cafe, she can only hope that change is kind. by Azure Notion 23,717 words · 712 · 7
Nothing Left to Lose Some things can't be changed. Starlight believes otherwise. by Freglz 6,367 words · 381 · 9
Sunflower - Life in Equestria A collection of side stories based on Project Sunflower: Harmony by Hoopy McGee 38,270 words · 742 · 19

Two more stories related to Sunflower, plus some more recent stories I've read and really like. See also the sequel to Unchanging Love, Unending Love!

EThe Change
MLP: FiM
Romance
Drama
Slice of Life
When two percent of a large city is suddenly, and without explanation turned into ponies, will April ever be able to get back what she lost?
Alt. Universe
OC
Pony Grove · 23k words · 23 3 · 798 views
ENothing Left to Lose
MLP: FiM
Drama
Sad
Some things can't be changed. Starlight believes otherwise.
Chrysalis
Starlight Glimmer
Freglz · 6.4k words · 381 9 · 5.8k views
EPom's Chapter — A Novelization of a Story That Doesn't Yet Exist
MLP: FiM
Them's Fightin' Herds
Adventure
An adventure detailing Pom's unwilling journey through Foenum for the Prophet's Key.
Other
AIPomgeon · 45k words · 31 0 · 733 views
TIt Takes a Village to Reform a Changeling
MLP: FiM
Comedy
Drama
Slice of Life
Mandy Carapace crashes into Ponyville, and has no intention of returning to the Hive.
Profanity
Alt. Universe
Twilight
Applejack
Spike
Celestia
Changelings
MattTOB · 50k words · 255 18 · 5.2k views
TUnending Love
MLP: FiM
Romance
Adventure
Drama
After trials and heartache, Firefly, undercover changeling love collector and wife, received a wonderful and joyous gift. But what will happen when the inevitable fallout of the failed Canterlot invasion reaches her home?
OC
Chrysalis
Changelings
Azure Notion · 169k words · 573 9 · 5.7k views
EThe Nemesis
MLP: FiM
Slice of Life
Starlight and Trixie have a debate concerning their relationship to Twilight
Trixie
Starlight Glimmer
James Pwyll · 2.1k words · 191 5 · 2.6k views
TFine Print
MLP: FiM
Romance
Drama
Slice of Life
Tracy needed somewhere to stay, how was he supposed to know that it was in another universe? Now he'll somehow have to hold down a job on Earth while living as a pony in Equestria. It's either that, or say goodbye to being human.
Profanity
Human
OC
Roseluck
Starscribe · 142k words · 1,816 51 · 20k views
EHigh Flight
MLP: FiM
Slice of Life
Cherry Berry's first flight attempt
Other
Cherry Berry
Admiral Biscuit · 1k words · 114 2 · 1.9k views
EThe Ending of the End - Love and Tolerance Edition
MLP: FiM
Adventure
Equestria faces its most dire threat yet as Grogar and his legions march upon Canterlot. Meanwhile, Cozy Glow, Chrysalis, and Tirek prepare to betray him and seize power themselves. Can the Mane 6 save Equestria?
Main 6
Chrysalis
Tirek
Cozy Glow
Grogar
StarlightisVERYcute · 100k words · 230 12 · 6.1k views
TUnchanging Love
MLP: FiM
Romance
Drama
With the advent of the Canterlot wedding, change is coming. Sweet Leaf is an undercover changeling love collector, wife, and co-owner to the Sweet Roast Cafe, she can only hope that change is kind.
OC
Changelings
Azure Notion · 24k words · 712 7 · 7.5k views