In the library section of Hivory Towers, a book can be found with the title "Jet Packs and Butlers: Your First Investment". This is a reference to one of the possible lines spoken by Conker after collecting a wad of cash in Conker's Bad Fur Day.
As a professed fan of the Banjo-Kaoozie series, Youtuber Jonathan Aryan "Jon" Jafari (Jontron) was originally going to voice a character for the game. Due to a controversy over his political views, however, Playtonic removed Jontron's voice from the game in a mandatory day-one update. He would have originally voiced a character stuck in an outhouse in the "Galleon Galaxy" level.
It's possible that the emblem on Captial B's staff is designed after the Empty Honeycomb collectible from Banjo-Kazooie.
At the end of the game's E3 2016 trailer, a Jiggy from Banjo-Kazooie can be seen in one of the character's drink glasses. This nod to some of the senior developers' previous series seems to be completely removed from the final game however, as Playtonic likely do not have the rights to use it.
During Yooka and Laylee's first meeting with Kartos, Laylee refers to him as the "God of Ore". This is a reference to the Sony-exclusive franchise God of War, as well as its' main protagonist, Kratos.
Before deciding on having the game's protagonist as a chameleon and a bat, Steve Mayles considered having a tiger as they were great looking animals, but decided against it as he was deemed too much of a hero when all his past characters were more like underdogs. He even considered having a witch and a broom with eyes before the final decision.