- In Rusty Bucket Bay, the Rusty Bucket has "Twycross, England" on the back of it. Rare is based in Twycross, England.
- In Witchyworld, in the Dodgem Dome Lobby, there is a constellation in the background, shaped like Rare's website mascot, Mr. Pants.
- In Jolly Roger's Lagoon, in the UFO, Kazooie asks the aliens if they need to "phone home", which is a reference to the movie E.T. Also, the lockers in the area with D. Jones' Locker have the names of Banjo-Tooie team members. The Davy Jones' Locker is a reference to the popular term.
- Also in Jolly Rogers Lagoon, Kazooie asks the aliens if one of them is named Elvis. This is a reference to a famous Perfect Dark character, Protector One, or Elvis the Maian.
- In Grunty Industries, there are crates labelled "Defective Goods: Ship to Twycross, England". Rare is based in Twycross, England. There are also crates labeled "TK-421" and "AA-23". TK-421 is the designation of one of the stormtroopers from Star Wars, and AA-23 is Leia's detention block in the same movie.
- Also, if the character talks to Loggo a second time before unclogging him, Kazooie suggests that he call a plumber, saying that Mario ("that Italian gentleman" in the XBLA version) is free at the moment, with Loggo saying he probably doesn't do that kind of work anymore.
- In Hailfire Peaks, Boggy and his family return, living in a new igloo. Showing on Boggy's TV, is static, with an image of Mr. Pants appearing every few seconds.
- There are two ice cubes, George Ice Cube and Mildred Ice Cube, who appear in Cloud Cuckooland and Hailfire Peaks, respectively. Both names are a reference to the 1970s British sitcom, Man About the House.
- In Cloud Cuckooland's central cave, there is a safe named Superstash, who guards a Jiggy. His combination is 1984, which he describes as "a Rare date". Rare was founded in 1984.
- In the Tower of Tragedy game, the wrong answer to the name of the floater creature is "Floatsum Jetsum". This is possibly a reference to the eels from The Little Mermaid, Flotsam and Jetsam.
Banjo-Kazooie: Nuts & Bolts
- A blueprint you can buy from Humba is the "Humba Union Jack", which is a vehicle made to look like a British flag (Rare's headquarters is in Twycross, England). In the description of it when you're buying it, she wonders if the Rare team is too patriotic.
- Each world (except Showdown Town and Spiral Mountain) has an intro that references the intro of an old TV show. Nutty Acres references the show Dallas, LOGBOX 720 references Buck Rogers in the 25th Century, Banjoland references The Love Boat, Jiggoseum references Dynasty, Terrarium of Terror references Lost in Space and L.O.G.'s Lost Challenges references The A Team.
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