GoldenEye
Ol' Bond went through more changes than most games during development. 'Lost' secrets include the abandoned Citadel multiplayer level (which exists as bare geometry within the cart), unused characters, vehicles, portions of missions and non-functioning items.
Mystery Island
On the far side of the reservoir in the first level, there's a strange, unreachable island. On the near side, there's a pier with no obvious function. At one point there would have been an objective involving reaching the island by boat, but it was removed for the sake of streamlining the gameplay in the opening scenes.
All Bonds
At one point, the multiplayer component of the game was going to feature classic Bonds - all the actors who had played 007 in the past. However, when it was discovered that the likes of Sean Connery, Roger Moore and Timothy Dalton would probably require payment for their image rights, the idea was dropped. The low-res photos that would have been used on the character selection menus remained, tucked deep within the finished cartridges and accessible only via Action Replay hacking.
Cheat codes
Nintendo games rarely include cheat codes, and GoldenEye was thought to be no exception to the rule. One multiplayer code was revealed early on, but it was years after the game's release that hackers uncovered a whole array of other codes, presumably left over from the game's beta testing stages, including the missing '24th cheat' - Line Mode.
New Super Mario Bros
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Early screens show the game looking just a tad bland, with backgrounds that didn't appear in the final product and the function of the lower screen either undecided or deliberately kept secret. Videos from around this period show co-operative multiplayer, with the brothers actually playing on normal levels. Whatever happened to that?