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Final Fantasy V featured Boko, or Boco, as an important non-player character for Bartz introduced early on in the game. His role is diminished almost immediately after his introduction and he does not appear again until much later in the game, but I thought that this was an especially notable role for chocobos in the series.
II, as otherwise, there wouldn't be other Chocobos in the rest of the series. :p ;)
Final Fantasy IX did it best with hot n cold. Although FFVII is more memorable to me. I still have to say FFIX did it better.
VII! The races were just lovely. And I just loved the way you discovered the colored chocobos through the Chocobo Wise's hints. I hated, though, that the green chocobo gives you so much of a reward: Ancient Forest without Ultima WEAPON, Lucrecia Cave without Submarine and (quite probably) the very best materia in the whole game.
Maybe they should've swapped Mime and KotR.