In the European and American versions of the game, King Boo has an empty text box displayed when he is confronted by Yoshi in Big Boo's Haunt. This means Yoshi could have originally entered Big Boo's Haunt without the requirement of selecting Mario, Luigi, or Wario.
The Korean version of the game lacks a backlight setting and the Rec Room seen in other versions.
In the South Korean version of the game, there's a Yellow ! Block that appears on the castle roof right next to the Red ? Block. Hitting it from underneath will give the player an infinite amount of extra lives and will not disappear, allowing them to easily acquire 100 lives. This was removed in all other versions of the game.
Found within the game's data is an unused Red Koopa Troopa that can only appear through hacking methods. Unlike the green Koopa Troopas found in the game, the red ones will attempt to run at the player and knock them around similar to Bullies. When knocked out of their shells, they'll slowly walk back into them instead of panicking like the green ones do. In addition, their shells cannot be ridden. Instead, they will only slide along the ground like in previous Mario games, killing enemies in their path until they break against a wall. If a Red Koopa Troopa is eaten by Yoshi, he'll spew out fire like he does when eating one in Super Mario World.
By alternating between Mario and Yoshi's drawing icon three times on the title screen, Mario will transform into a drawing of Luigi.
Coincentration's sprite set contains some Super Mario Advance 4 sprites, which aren't used in the final game. Coincentration's internal name is "wrecking_crew", a reference to the NES game of the same name. The mini-game uses this name in New Super Mario Bros. as well.
The Nintendo 64 version of the room containing the entrance to The Princess's Secret Slide is still part of the in-game's castle model, complete with a sign and a functional warp to the Secret Slide. The door leading to this room was simply changed to lead to the new version of the room.
"Wing Mario Over the Rainbow" is the only course that does not have a Luigi Cap, even when Luigi is unlocked.
In the game's data, replacing a file called "0000_PLAYER" with another file spawns a clone of the player that follows his movements. It takes on the appearance of Mario, but will shift into a different character when hit (spawning with a Mario cap).
The Bob-Omb Battlefield mission "Shoot To The Island In The Sky" from the Nintendo 64 version was removed in Super Mario 64 DS, and replaced with the mission "5 Silver Stars".
At the start of the game, Yoshi can be seen sleeping on top of the castle. This is a reference to where you found him after you got all the stars in the original Super Mario 64.
When first announced, Super Mario 64 DS was named "Super Mario 64 x 4", and seemed to feature gameplay where the player would utilize all four characters at the same time. This early build was shown at E3 2004 before being altered to be more like the original.
In the minigame "Loves Me/Loves Me Not", the tune that plays during a "REALLY LOVES ME!" is the Recorder theme from The Legend of Zelda.
Each boss in the game has a specific piece of dialogue based on who you're fighting them as. Even though Yoshi can't actually fight Chief Chilly, there is still dialogue programmed in for that fight.