My Little Pony XCIX: Leakier Than A Changeling Bathtub!

[Topaz]

Topaz' Traditionally Tardy List of Pony tabletop RPGs:

Hasbro's Officially Licensed My Little Pony Friendship is Magic TRPG --

Tails of Equestria, from River Horse PDF via DriveThruRPG (Facebook Page)

Stand-alone Games --

D20 Based:
Courage is Magic (2.2 The Moon Sets Edition!) (Very Heavily Modified D&D4 based)
Heroes of Equestria (D&D-ish)
Pony Tales: Aspirations of Harmony (d20 meets Final Fantasy style)

D6 Based:
Magic of Equestria (a system in progress designed for play-by-post)
My Little Pony: Roleplaying is Magic, Season Four
Pony Tales the RPG (Open d6 based)
My Little Pony: Friendship is Magic, The Roleplaying Game (Older game using a D6 dice pool)
Puzzles and Ponies (Simple 1d6 game)

D10 based:
Sereg's Pony RPG (D10 dice pool)

D100 (percentile dice) based:
Fallout: Equestria RPG
Older, different Fallout:Equestria RPG
Fallout: Equestria PNP

Multiple die type based:
Seeds of Harmony (Translated from Italian) (Discussion on the Equestria Daily Forum)
My Little Heroes AKA Hooves of Heroes (Original ODT file) (PDF version)
Ponies: The Roleplaying Game

Dice Pool Based (Ubiquity System):
Roan – Pulp Adventure RPG (Commercial "Equine Action Adventure in a world of Pulp Fiction")

Playing card based:
Friendship is Magic, the Tabletop RPG (GitP forum)

Commercial Card-based Dungeon Adventure Game:
Buck: Legacy

Supplements for existing systems --

Ponyfinder, a commercial Pony-based Campaign Setting for Pathfinder (Main book, has many supplements)
Pony Races for Pathfinder (Old)
2012 Fan Pony-Pathfinder thread on Paizo forum

The Ponyfinder Setting Book for D&D 5th Edition
Planeshift:Equestria, a Pony sourcebook for D&D 5th Edition (New version 1.10)
Roleplaying in Equestria for D&D Fifth Edition and associated Bestiary and Artifact book
Digo's Pony Races for D&D 5e (Discussion on GitP)

Ponies for D&D 4e

Dungeons & Dragons: Friendship is Magic (Ponies for D&D 3.5)
Pony Races for D&D 3.5 (GitP forum)
Ponies! My Little Pony: D20 adaptation

The Conversion Bureau (uses Microlite 20)

Rarity's Marvelous Wish-Granting Chapeaux (RPGnet forum, FiM using The Chuubo's Marvelous Wish-Granting Engine RPG.)

The Savage World of My Little Pony (uses Savage Worlds)

My Little Pony meets Exalted tumblr

Shadowtrot by Digo Dragon (uses Shadowrun 4e) (Original Nightmare Run)

The Mane Six for FATE Accelerated (RPGnet forum)

MLP:FiM for Burning Engine/Mouse Guard (Discussion on RPGnet)

Unknown Ponies: Failure is Awesome (uses Unknown Armies)

Don't Rest Your Hooves (uses Don't Rest Your Head)
Don't Hate Your Friends (Don't Rest Your Head hack, RPGnet forum)

My Little Legend (uses the Legend RPG from Rule of Cool RPGs)

Ponies for Oz (uses Adventures in Oz: Fantasy Roleplaying Beyond the Yellow Brick Road)

Further contributions and updates welcome!