Inside the Dodgems Dome in Witchyworld, looking out of the window you can see a constellation of Rare's then mascot, Mr. Pants. He also makes an appearance on a TV in Hailfire Peaks, inside Boggy the polar bear's igloo.

Inside the giant trash can in Cloud Cuckooland, You can find a giant milk carton with Tooty's face on it which reads "Missing. Last seen in Banjo Kazooie." This is a joke that references the fact that she does not appear anywhere in the game.

In Banjo-Tooie at Jolly Roger's Tavern, you can find a man by the name of Captain Blackeye. He repeatedly states "Once, I had a dream..." and tells of a bear who stole his glory. This is a reference to Project Dream, the first version of Banjo-Kazooie. He was meant to be the main antagonist of the game.

There was originally a mode called "Bottles' Revenge" which would allow for a second player to antagonize Player 1 in the main game.

In it, the evil spirit of Bottles is able to free himself after being killed by Gruntilda. Whilst this mode is enabled, Player 2 can take control of a nearby enemy to attack Banjo and Kazooie.

While this mode was cut from the game, it can still be accessed through the use of a cheat device. Devil Bottle's dialogue portrait also still appears in the Tower of Tragedy quiz game at the end.

A few of Banjo-Tooie's worlds were originally planned for its predecessor, Banjo-Kazooie, such as the fire side of Hailfire Peaks and Glitter Gulch Mine. Many of these were cut primarily because of time constraints.

Gobi mentions leaving for the "Lava World" in Click Clock Woods, which adds up as Gregg Mayles' concept art for the cut lava world shows that Gobi would have been present. Gobi would eventually live up to his promise by appearing in the fire side of Hailfire Peaks in Banjo-Tooie, after being freed in Witchyworld.