Topaz' Traditionally Tardy List of Pony tabletop RPGs:
Complete Games --
D20 Based:
Courage is Magic (1.15) (Very Heavily Modified D&D4 based)
Heroes of Equestria (D&D-ish)
Pony Tales: Aspirations of Harmony (d20 meets Final Fantasy style)
D6 Based:
Pony Tales the RPG (Open d6 based)
Ponies & Parasprites, Season Two (D6 total based)
My Little Pony: Roleplaying is Magic, Season Three (New Season Three Mechanics! Uses 2 or 3 D6, earlier editions used D20)
- And Rater202's Capricorn race for RiM Second Edition
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:
Ponies: The Roleplaying Game
Playing card based:
Friendship is Magic, the Tabletop RPG (GitP forum)
Suppliments for existing systems --
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)
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 v2 (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!