Chris Marlow, a software engineer working at Rare, said that "there was an awful lot of content and there were lots of fun ideas, but it just really wasn't gelling as a finished game." So after some back and forth between the workers, they turned...
The unreleased Twelve Tales Conker 64 which was going to be a sequel to Conker's Pocket Tales, which never came to be since they wanted the game to be more for maturer audiences.
There's some early content for Super Mario 64 and Ocarina of Time that has surfaced over the years. In the case of SM64, test levels and even a Luigi model have come to light. For OoT, early environments and prerenders have been found. Anything...
New Super Mario Bros. This old prototype still amazes me and apparently there's a cut scene at the end where the player controls Bowser and I would love to see if that's still somewhere in some of the betas.