Keep Circulating the Tapes: Before the Wii remake came around, getting any kind of re-release together was a copyright nightmare, requiring Nintendo (the game's former publishers), Microsoft (Rare's present parent company) and Activision (the current owners of the Bond license) to all agree on who gets the biggest share, which has kept this game off both the Virtual Console and Xbox Live Arcade. Perfect Dark, on the other hand, had no such issues - then again, that one was solely an XBLA release and had nothing to do with Bond, removing a few hurdles.
Throw It In: The multiplayer aspect of the game was a major afterthought and would have not been in the game at all if it wasn't for a programmer or two that decided to create it at the last minute. Not only was the multiplayer made in just a few hours, it was done without Rare or Nintendo knowing about it before the game was ready to be released to the market. Rather than reprimand the programmers who coded the multiplayer, they basically said "Screw it, keep it in". The decision would prove to be a good one since not only was the multiplayer touted as one of the best things of the game, but it would also set the standard of first person shooter multiplayer games on consoles.
Urban Legend of Zelda: Rumors persisted about the purpose of the island across from the Dam at Arkhangelsk. Using a Gameshark code to walk there reveals that it has nothing but a non-working turret gun and an empty guard tower.
The Citadel was thought to be a myth... but was later discovered to really exist in the game's code as a testing level.
Then there's the infamous "All Bonds" option...
For the last time, Oddjob and Mayday do not appear in single-player mode, and Xenia is not anywhere in the Frigate level.
That one is justified, since the Instruction manual and in-game briefing say they are, respectively.
Another one caused by the instruction manual is mention of a weapon called the "Spyder", which was often assumed to be one of the weapons shown on the back of the case. The confusion stems from the terminally-useless Klobb, originally meant to be called the Spyder until the devs realized that was the name of another real-life gun; this name change came about late enough in development that the manual still refers to the gun as the Spyder. The weapon on the back of the case is actually one of the beta models for the KF7 Soviet rifle.
What Could Have Been: Several maps would have made it into the multiplayer mode, but were Dummied Out. Using a Gameshark or the like to unlock the maps show that they run fine for the most part, but the Cradle map caused massive slowdown due to the size of the level. The Statue map, while it runs just fine, was simply too dark and made it difficult to track down other players.