In Jolly Roger's Lagoon is a sunken space ship near the Atlantis Area. Upon entering the UFO, Banjo and Kazooie meet four aliens, and Kazooie asks "Are any of you called Elvis?" This is a reference to another Rareware Game, Perfect Dark, in which there is an an alien named Elvis. This in turn refers to a number of theories that the entertainer Elvis Presley was an alien.

In 'the Workers Quarters' of Grunty's Industries, you can find Loggo in the men's bathroom, who has something clogged inside him. If you talk to him for a second time before unclogging him, Kazooie will bring up the option of calling a plumber and mentions 'Mario' by name. In the XBLA version, the reference is changed to "that well known Italian guy" as Microsoft could not use Mario's name.

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.

Banjo-Tooie's Terrydactyland contains a sub area, dubbed the Stomping Plains, which in turn is home to the Stomponadon, a seemingly theropod dinosaur so enormous in scale that only its foot is visible. It functions as the main obstacle of this area as, hence its name, it will try to stomp on Banjo & Kazooie as they attempt to traverse the plains. The concept behind Stomponadon had its origins from Banjo-Kazooie's earliest prototype game, Dream: Land of Giants; footage of Dream released by Rare for the first time in 2015 showed that Edson (who was replaced by Banjo in the final game) was to have encountered a similarly large dinosaur that would try to crush him with its feet.

Donkey Kong makes a cameo in the original Nintendo 64 version of Banjo-Tooie in the form of a plush doll held by one of Bottles' children, Goggles, obviously referencing how Rare developed games for both franchises at the time. While this doll would reappear in the game's Xbox Live Arcade remaster in 2009, its texture was modified, with DK's brow ridge replaced by generic googly eyes to avoid any potential legal issues with Nintendo. The original texture and doll design would later be restored for Banjo-Tooie's re-release on Nintendo Switch Online in 2024.