Superstar Saga and Bowser's Inside Story. I've put SSS on top in the past, especially in contexts where having a tie kind of defeats the point, but really I love them both equally for both similar and different reasons. Fawful is the big reason they have in common. Superstar Saga has all the rest of the Beanbean characters like Cackletta and all the crazy shenanigans that happen there (including the twist of Bowletta, call it cliche now but back then I found it really creative, not the game's fault a bunch of Mario games ripped it off later in less interesting ways), while BIS did a fantastic job of portraying Bowser's side of the story and transitioning Fawful from a minion to calling the shots himself. The Dark Star was awesome too, I tend to love it when the Mario RPGs have dark evil artifacts that could spell certain doom for all.
Dream Team follows closely behind, followed by Partners in Time. The only one I don't like is Paper Jam.