Topaz' Traditionally Tardy List of Pony tabletop RPGs:

Complete Games --

D20 Based:
Courage is Magic (New 2.1 Monsters 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:
My Little Pony: Roleplaying is Magic, Season Four (New Update!)
- And Rater202's Capricorn race for RiM Second Edition
Pony Tales the RPG (Open d6 based)
Ponies & Parasprites (D6 total based)
My Little Pony: Friendship is Magic, The Roleplaying Game (Older game using a D6 dice pool)
A different My Little Pony: Friendship is Magic, The Role-Playing Game (2D6 based, meant to be run for younger players)
Puzzles and Ponies (Simple 1d6 game)

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

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

Multiple die type based:
My Little Heroes AKA Hooves of Heroes (Original ODT file) (PDF version)
Ponies: The Roleplaying Game

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

Supplements for existing systems --

Roleplaying in Equestria for D&D Fifth Edition
Digo's Pony Races for D&D 5e (Discussion on GitP)
Ponies for D&D 4e
Pony Races for Pathfinder
Ponyfinder thread on Paizo forum
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.)
All The Pretty Little Horses! (uses Apocalypse World) (Discussion on RPGnet.)
The Savage World of My Little Pony (uses Savage Worlds)
My Little Pony meets Exalted tumblr
NightmareRun by Digo Dragon (uses Shadowrun 4e)
Friendship is FATE rules & Discussion Blog (uses FATE Accelerated)
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!