On the bottom floor of Boggy the polar bear's igloo in Hailfire Peaks, on two of the kid's beds are the Perfect Dark logo and Banjo-Kazooie promotional artwork.

In Jolly Roger's Lagoon, there is a pig named Chris P. Bacon who is trying to take underwater pictures of the ruins. Looking closely at the camera he's using reveals that it's actually a Game Boy Color with a Game Boy Camera attached.

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.

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.