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 Grunty Industries, there is a small chance that when going to the Worker Quarters, the player can spot light emanating out of a restroom where a worker rabbit can be heard taking a rather huge "dump".

The combination code to obtain the Jiggy belonging to Superstash the Safe in Cloud Cuckooland's central cave is 1984, which the safe describes as "a Rare Date". This is a reference to the year that Rare was founded, 1984.

One of the main characters in the game is the military brother of Bottles, Jamjars. This name was actually first used in Banjo-Kazooie during the opening training. As the player is testing out Kazooie's beak barge, Bottles comments that Kazooie is useful for something, to which she retaliates with, "I'm trying this move out on you next, jam jars!" The term comes from slang for large glasses with thick lenses.

It's possible to slow down the Star Spinner in the Space Zone section of Witchyworld by launching a Grenade Egg at the control panel to the left of the entrance.

Sabreman can be found on the ice side of Hailfire Peaks. Sabreman is a an old character from the Sabreman series, developed by Rare under their original name of "Ultimate Play the Game". Sabreman references his old games when the player unfreezes him, saying that he has been trapped in there since 1984, the release year of his first game Sabre Wulf.

Once the player takes Sabreman back to his tent on the fire side of Hailfire Peaks, he will begin to ramble about perhaps riding a dolphin. This may refer to the code name for the GameCube.

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 Xbox Live Arcade version, the reference is changed to "that well known Italian guy" as Microsoft could not use Mario's name.

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. This is retained in the Xbox Live Arcade version of the game despite it being on a console from a rivaling company.

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.