Troubled Production: An astounding example of this. There's loads of missing content, unused ideas, and whole models that ended up getting thrown out. As a result, the game is pitifully unfinished, even if it's pretty fun.
Collecting yellow gems unlocks "unseen extras" which apparently feature ideas and concepts that never made it into the final version. This is lampshaded by Cortex once: "We were going to visit two dimensions, but... we ran out of time."
Several hours worth of content was removed from the game, including several returning characters, new levels, and a Villain Song for Dr. Cortex entitled "Take a Walk Inside My Brains". Two members of the development team released a great deal of information on these removed items, which can be viewed here.
At least two direct sequels were also planned, but never made it past early planning due to Traveler's Tales' Oxford unit shutting down.