Bowser's Inside Story
Chrono series (since it's not fair for me to compare the two)
FF9
Suikoden series (although I felt III was kind of a dud and I never played V)
Pokemon G/S were my favorites, but the series in general is great
Runner ups!
Grandia (I've only finished the first one though)
Kingdom Hearts II
I want to put Skies of Arcadia in the list but I never finished it
Dragon Warrior (Of the first two I liked the first better tbh)