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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 · 5,228 · 92
ARTICLE 2 An alien crash lands in Equestria. It calls itself human. by Muppetz 228,756 words · 5,217 · 179
Arrow 18 Mission Logs: Lone Ranger A mission to investigate a far off world takes an interesting twist. by AdmiralTigerclaw 66,018 words · 6,320 · 87
Anthropology Lyra is determined to find out the truth behind the mysterious legends of humans. by JasonTheHuman 130,415 words · 8,571 · 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 · 1,270 · 36

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 · 2,592 · 55
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 · 2,546 · 53
Arrow 18 Mission Logs: Sparkle's Notes Companion Text to Arrow 18 Mission Logs: Lone Ranger by AdmiralTigerclaw 14,955 words · 2,857 · 42
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 · 4,147 · 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 · 1,698 · 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 · 1,836 · 27
The Nemesis Starlight and Trixie have a debate concerning their relationship to Twilight by James Pwyll 2,054 words · 198 · 6
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 · 731 · 7
Nothing Left to Lose Some things can't be changed. Starlight believes otherwise. by Freglz 6,367 words · 401 · 9
Sunflower - Life in Equestria A collection of side stories based on Project Sunflower: Harmony by Hoopy McGee 38,270 words · 746 · 18

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!

ESomeone Had Tae Do It
MLP: FiM
Them's Fightin' Herds
Adventure
Chosen as champion for speaking up, Pom and her dogs embark on a journey she feels utterly unprepared for.
Galgus · 38k words · 13 1 · 340 views
EA Day of Rest
MLP: FiM
Them's Fightin' Herds
Adventure
Paprika finds Arizona unconscious and helps her recover, whether she likes it or not. Set directly after Arizona's chapter, with minor retcons.
Galgus · 6.1k words · 14 0 · 614 views
ECooling Down
MLP: FiM
Them's Fightin' Herds
Adventure
Velvet gains a new perspective on her defeat with Arizona and Paprika arriving with a crucial clue.
Galgus · 42k words · 569 views
EBook of Lore - Shanty's Chapter
MLP: FiM
Them's Fightin' Herds
Adventure
A Them's Fightin' Herds story, and an attempt to write a Book of Lore entry for Shanty.
Galgus · 1.5k words · 11 0 · 356 views
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 · 897 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 · 401 9 · 6.3k 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 · 33 0 · 872 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 · 263 18 · 5.7k 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 · 596 9 · 6.1k 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 · 198 6 · 2.8k views