Despite being developed in Japan, the Japanese version is all in English with Japanese subtitles.
There is a major glitch in the game that allows you to access a sub world, sometimes called the "Blue Hell". The game physics are dropped down (meaning, for example, you can move around normally underwater, but if you jump it will revert to normal) and you can access many areas with little or no effort, particularly the Yoshi fruit boats.
In the attic of the Hotel Delfino, the janitor complains about the ghosts, wishing someone would come and "suck them up in a vacuum cleaner". This is a reference to another Gamecube title, "Luigi's Mansion", where Luigi did indeed suck up ghosts in a vacuum cleaner.
In the Japanese version of Super Mario Sunshine, "Isle Delfino" is known as "Dolphic Island". When a player retrieves a Shine Sprite, the "message" says "Shine Get!" instead of the English "Shine!"
Beatles fans, rejoice: there's a reference to this band on this game. I know it's kinda obvious to state so, but I swear I nearly cried when I saw a yellow submarine on the Ricco Harbor stage.
This game is set on a tropical island named Isle Delfino. "Delfino" is Italian for "Dolphin", which was Gamecube's prototype's name. And there are some stuff written in Italian around the game, like "Benvenuto" ("welcome"), etc.