I admit I have a soft spot for FFXIV's own Bo Down (the 'western' themed version used for the Chocoporter and rental chocobos). Also the Gold Saucer chocobo racing theme Sport of Kings and the GATE theme Gateway to Paradise are actually remixes of the FFVII chocobo themes Fiddle de Chocobo and Electric de Chocobo respectively (the later which is one of my favourites).

FFXIII's Chocobos of Cocoon is a unique twist though - it's a pop song with earworm lyrics. FFVIII's Mods de Chocobo (featuring a cameo from Uematsu's own Fender Telecaster guitar no less), FFVI's Techno de Chocobo and FFX's Brass de Chocobo were also very good.