Hands down, it would be Lucifer's Call. AKA, Shin Megami Tensei: Nocturne. Honestly, even with the FF games thrown in it would break my top 3 RPGs I think. I just love the tone, the minimalist story, the battle system, the difficulty, and the music. It's an amazing game. I can't wait for Shin Megami Tensei IV, hopefully it will make it to Europe one day!
Runners up would include Morrowind, the Pokémon series as a whole, and Tales of Symphonia.
Runners up would include Morrowind, the Pokémon series as a whole, and Tales of Symphonia.