Author Appeal: Sea salt ice cream is an actual product sold at Tokyo Disneysea that Nomura enjoys. He imagined that it would be something the characters would eat over summer vacation, so it was put into the game.
Executive Meddling: According to Tetsuya Nomura, he had originally planned on only including characters from Final Fantasy titles he personally designed. He eventually caved in to the urging of the staff, which is how Setzer and Vivi were added to the game. The gamble perhaps didn't pay off as well as they would've hoped; Setzer, in particular, was criticized for heavily deviating from his original incarnation's personality, moreso than was par for the course in KH.
Before his name was revealed, fans took to calling Roxas the Blond-Haired Kid (BHK) or Dual-Wielding Unknown.
"Orgy XIII" for the entirety of Organization XIII.
Fans commonly refer to Xemnas as "Mansex" - an anagram of his name. This paved the way for Bigrax for Xigbar, E-Sexual for Lexaeus, and finally Rentx-a-ho (Rents a ho) for Xehanort.
Xemnas in his Final Boss outfit is Zebraman due to its black and white coloration.
Pete is given the nickname Captain Ass-Zipper, due to the bizarre placement of the zipper on his outfite.
Chip Cheezum and friends popularized "Dogstreet" for Pence, named after the writing on his shirt.
Fandom Nod: In addition to all the Disney/Final Fantasy references, there is a literal fandom nod during Cloud and Leon's snark-fest in the sequel. As they do their Back-to-Back Badasses moment, it echoes the rivalry between fans of their respective games.
Role Ending Misdemeanor: Between Kingdom Hearts I and this game, Billy Zane starred in the Turkish film Valley Of The Wolves: Iraq. It portrayed American soldiers fighting in Iraq as monsters, earning severe criticism and getting the movie declared "Anti-American Propaganda" by many critics. Disney decided that didn't want him working on the series anymore due to the controversy, so his role as Ansem, Seeker of Darkness was recast to Richard Epcar, including for flashback scenes.
Axel was originally supposed to die at the end of the prologue. The development staff liked him too much to remove him from the story that early, so his role was expanded.
Buzz and Woody from Toy Story were going to be a Summon in the Final Mix version, but were scrapped. Their unfinished models are still in the game files.
Early trailers suggest that the outside walls of Hollow Bastion's castle from the first game would be playable.
Variations on the Behemoth and Wyvern Heartless were present in the Battle of 1000 Heartless in older trailers.
Xemnas was going to have two more forms for the final battle, the "King" and "Centaur"◊. They would have him apparently breaking up and surrounding himself with chunks of the Dark City to create something akin to the giant dragon that is fought in the final game.
The game was planned to feature battles against all of the Organization members in the Coliseum, but they had to be dropped due to lack of time. This was re-imagined into the Data battles found at the end of the Cavern of Rememberance in the Final Mix version.
David Warner wanted to reprise his roles as the MCP and Sark, but he was not able to since he was committed to another role at the time.
There is an unused version of the Final Fantasy IX world map theme in the game's coding. There are a few theories for it: some think it was going to be used for the fight with Vivi, and others think that Vivi (or even other characters from FFIX) was going to play a larger part in the story.