Topaz' Traditionally Tardy List of Pony tabletop RPGs:

Pony Tales: Aspirations of Harmony (Homebrew, d20 meets Final Fantasy style)
Ponies & Parasprites, Season Two (Homebrew)
My Little Pony: Roleplaying is Magic, Season Two (Homebrew)
My Little Pony: Friendship is Magic, The Roleplaying Game (Homebrew)
Pony Tales the RPG (D6 system based)
Friendship is FATE (FATE system)
The Savage World of My Little Pony (Savage Worlds)
Puzzles and Ponies (Homebrew)
Ponycraft (3D6 Homebrew)
Friendship is Magic, the Tabletop RPG (Homebrew, these forums)
Sereg's Pony RPG (D10 Homebrew)
Unknown Ponies: Failure is Awesome (Unknown Armies)
Don't Rest Your Hooves (Don't Rest Your Head)
Don't Hate Your Friends (Don't Rest Your Head hack, under discussion)
Ponies! My Little Pony: D20 adaptation
Pony Races for D&D 3.5 (These forums)
Ponies for D&D 4e
Ponyfinder thread on Paizo forum
Storyteller based Pony RPG tumblr
Fallout: Equestria (Fallout Tabletop d100 project from [email protected] )
Fallout: Equestria PNP (Revised) (Homebrew, unrelated)

Further contributions and updates welcome!