I named Cloud after me the first time I played, other than that the chocobos were the only unique names

they were creative, if i do say so myself

Regular Male Chocobo : ChocoM
Regular Female Chocobo : ChocoF
Blue Male Chocobo : BlueM
Blue Female Chocobo : BlueF
Green Male Chocobo : GreenM
Green Female Chocobo : GreenF
Black Chocobo : Blacky
Gold Chocobo : Goldie

I amaze myself sometimes...