Executive Meddling: As pointed out by co-designer Martin Hollis, Nintendo had a hand in toning down the violence of the game, the most notable change being the removal of the blood you'd expect when killing an enemy (ironically, they kept the "Blood-flowing-down-the-screen-as-you-die" aspect intact).
Keep Circulating the Tapes / Screwed by the Lawyers: 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 (and by extension Activision), removing quite a few hurdles.
Sleeper Hit: One of the definitive examples in video gaming. It received almost no pre-release coverage, had a lackluster showing at E3 1997, was based on a movie that came out two years prior, and was developed almost as an afterthought, with the dev team consisting of 10 inexperienced college students. But then it was released, and was an immediate smash hit both critically and commercially, becoming the third best-selling game for the N64 (and the second-best selling N64 game in the US, behind only Super Mario 64.)
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 gunnote a lesser example involves rumors of another weapon called the "Skorpion", which is just the Klobb's real-life name; 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.
For years, licensing issues and Rare moving from Nintendo to Microsoft made rereleasing this game a complex issue. However, at one point Microsoft developed a enhanced port (just like with Perfect Dark) and approached Nintendo with a compromise allowing the game to be released on both the Xbox Live Arcade and Wii Virtual Console, but Nintendo declined for unknown reasons.
The All Bonds cheat allowed every player in multiplayer to play as Bond based on different actors that portrayed him over the years. The cheat got Dummied Out due to Rare being unable to secure permission from the actors to use their faces in the game.
The game was originally an on-rails shooter in the style of Virtua Cop before it became a first-person shooter.
According to co-designer Martin Hollis, Nintendo was dissatisfied with the violent content with the game and allegedly tried to make it where the villains aren't actually killed. At one point, Shigeru Miyamoto suggested to the development team that the game end with Bond shaking hands with the enemies at a hospital. Say what you want about that, but that's hilarious as hell right there.