In the skip outside Banjo's house, removing all of the junk from it reveals some unusual objects referencing other Rare games. These include a skeleton's skull from Grabbed by the Ghoulies, Fudgehog from Viva Piñata and a portrait of a bearded old man, possibly Sabreman, one of Rare's earliest characters. There's also a sign with the Rare logo on it, Banjo's banjo, a pink toy dog and what appears to be the Ice Key from the infamous Stop 'N' Swop feature. It should be noted that these objects are part of a texture on the bottom of the skip and cannot be picked up.

A Nintendo 64 can be seen next to Kazooie's Xbox 360 in the opening cutscene.

Sometimes the loading screens will play a slightly slower remix of the pause theme from Battletoads.

During the games opening, the radio behind Banjo and Kazooie plays 'Windy', the over world theme of Conker's Bad Fur Day.

After getting 6000 music notes, you can ask Bottles the truth of Stop N Swop. When you ask him, he says "I could tell you, but then I'd have to kill you, and we couldn't do that in a game of this rating. Put it out of your mind and think happy thoughts! Thanks for the notes!"

According to developer Gregg Mayles, Banjo-Kazooie: Nuts and Bolts was actually the third attempt at creating 'Banjo-Threeie', the third installment in the main line of the franchise. The first attempt was supposedly BanjoX, an unfinished build for the original Xbox which featured some new assets and items. The second attempt, was a re-make of Banjo-Kazooie with some twists, and would have possibly featured Gruntilda following the duo around different worlds and trying to outdo them.

One of the forms L.O.G. was to take was an old Ultimate! Play the Game cartridge. Ultimate! Play the Game was Rare's old name before it was changed.

One of the running jokes in the game is that "Grabbed by the Ghoulies" did not do well commercially. The best way to see this is in Banjoland. In the trashcan from the Cloud Cuckooland part of the park, there are many unsold copies of "Grabbed by the Ghoulies."