I honestly cannot think of a single "favorite" RPG that I have, I love so many...
I guess I'll just list ALL of my favorite RPG's...
Chrono Trigger
Suikoden 2 and 5
Final Fantasy VI, VII, IX, X and XII
KOTOR
Mass Effect
Baldurs Gate 2
Xenosaga 3
Persona 3 and 4
Planescape: Torment
Fallout 1, 2 and 3
Oblivion
Final Fantasy Tactics
The World Ends With You
Paper Mario: The Thousand Year Door
Tales of the Abyss
Lost Odyssey
Shadow Hearts: Covenant
Dragon Quest 5 and 8
Earthbound
Mother 3
Icewind Dale 2
Steambot Chronicles
Valkyria Chronicles
Skies of Arcadia
Fable 2
That's all I can think of right this second...
I've played a LOT of RPG's, pretty much the only genre I have no interest in are the Diablo style games and MMORPG's.