Banjo-Tooie's Terrydactyland contains a sub area, dubbed the Stomping Plains, which in turn is home to the Stomponadon, a seemingly theropod dinosaur so enormous in scale that only its foot is visible. It functions as the main obstacle of this area as, hence its name, it will try to stomp on Banjo & Kazooie as they attempt to traverse the plains. The concept behind Stomponadon had its origins from Banjo-Kazooie's earliest prototype game, Dream: Land of Giants; footage of Dream released by Rare for the first time in 2015 showed that Edson (who was replaced by Banjo in the final game) was to have encountered a similarly large dinosaur that would try to crush him with its feet.

One of the characters planned for Dream: Land of Giants before it was morphed into Banjo-Kazooie was Captain Cockeye, a friendly pirate character that was also described as being "a bit of a mad professor".

While this character wouldn't appear in the final Banjo-Kazooie game, Banjo-Tooie's character Pawno seen in Jolly Roger's Lagoon serves as a homage to him, by wearing his clothing as noted by former Rare character designer Ed Bryan.

Tiptup is a recurring NPC character in the Banjo-Kazooie series that, along with Banjo, also made his debut in Diddy Kong Racing in 1997. However, Tiptup was originally the name of a turtle in Dream: Land of Giants, the game that would eventually morph into Banjo-Kazooie. Halfway through the development of BK, the development team behind Diddy Kong Racing (or Pro-Am 64 as it was called before Diddy Kong was included later on) were in need of names for their racers, one of which happened to be a turtle, and thus it was given the Tiptup name. Tiptup was then incorporated into future Rare games like Banjo-Kazooie and Banjo-Tooie.

Before Rare decided to use Banjo to replace the character Edison (the main character of the canceled Project Dream project that would later become Banjo-Kazooie), they wanted the main character to be a rabbit.

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.

Banjo-Kazooie started development on the SNES and was titled "Project Dream" or "Dream: Land of Giants". The game was going to be an RPG, and the main character would have been a young man named Edison who had caused trouble with a group of pirates led by a man named Captain Blackeye.