One that isn't as frequently mentioned is the presence of alternate skins for the St. Petersburg civilians and female variants of both the civilian and scientist NPCs, all of which can be seen in the final casting reel after the credits but never show up during gameplay. The removal of the female NPCs was almost certainly bowdlerization by Nintendo, but it's not clear why the alternate male citizens were cut.
A number of alternate music tracks for several levels are present in the files, but not played in-game due to bugs, oversights, or just not having the room (the game only supports 2 music tracks per level). However, many of them can be heard in the multiplayer mode as tracks are randomly played.
Two multiplayer maps, Cradle and Statue, were Dummied Out due to technical issues (the Cradle map caused massive slowdown due to the size of the level, while the Statue map was simply too dark and made it difficult to track down other players). A Gameshark or the like can be used to play these maps, and besides the aforementioned issues they are effectively complete and functional.
A minor example; The "Egyptian" level was intended to have its sky turn red after killing Baron Samedi twice, but a bug in the code prevents this from occurring.
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 Bond franchise's "Blood-flowing-down-the-screen-as-you-die" aspect intact).
Keep Circulating the Tapes / Screwed by the Lawyers: The game has not seen any kind of rerelease since its original run, though it hasn't been for a lack of trying — An Updated Re-release of the game for the Xbox Live Arcade was in development and even partially completed. However, it fell afoul of legal issues; Microsoft, Rare (who at this point had been bought out by Microsoft) and Activision (who owned the Bond game license at the time) were all on board, but it was Nintendo (specifically Nintendo of Japan - their North American branch was allegedly okay with the rerelease) who flatly refused to negotiate, even when Microsoft offered to allow the game to be released on the digital storefronts of both the Xbox 360 and Wii. The fallout led to Rare and Microsoft using the engine they had created for the game for an Updated Re-release of Perfect Dark, while Activision would completely remake Goldeneye using Daniel Craig as James Bond.
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 development team consisting of 10 inexperienced college students, most of whom expected it to be overshadowed by the technologically superior Turok: Dinosaur Hunter. 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.) and a popular multiplayer title.
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.
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. Apparently the mission was originally going to take you to that island but the developers felt it broke the flow of the level too much so they removed any way to access it but left it visible to save time.
The Citadel, an unfinished level that was the source of many hoaxes through the community, 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" cheat that was said to unlock former Bond actors as multiplayer characters. (see What Could Have Been below for the truth of the matter)
For the last time, Oddjob and Mayday do not appear in single-player mode, and Xenia is not anywhere in the Frigate level. Although this 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.
The game was originally intended to be an on-rails shooter in the vein of Virtua Cop, before it became a first-person shooter. The game's unconventional aiming, where the crosshair is not locked to the center of the screen as in most shooters, is likely a remnant of this early plan.
It was intended that former Bond actors Sean Connery, Roger Moore, and Timothy Dalton would have been available in multiplayer as playable characters, and also would have been used in the Aztec and Egyptian bonus missions. Unfortunately, Rare was forced to cut them late in development due to legal concerns...but not before the developers had a 100-point deathmatch between the four Bonds.
Dave Doak: "Right near the end of development, a guy came in from EON who owned the Bond licence and saw we had put in Connery, Dalton and Moore as well as Brosnan. We thought it would be great for marketing and even some screenshots went out with Connery in his white tuxedo. Then an edict came down from on high and we had to get rid of the other Bonds, so on the day we had to take them out we played this epic deathmatch – first to a hundred kills – which went on for about three hours. Mark Edmonds played as Moore and won by one kill. It went down to the wire…”
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. This is in fact why the game features the cast credits at both the beginning and end - to give the illusion that the characters are actually actors and thus not actually being killed.
An interview with Martin Hollis also revealed that they had planned to include a ZX Spectrum emulator within the game in the guise of an arcade machine that would have allowed players to play Rare's ZX Spectrum games, but the idea was scrapped due to time constraints. The coding for the emulator is still in the game itself, but no games are present to use it with. This was later kept for Donkey Kong 64, giving players the ability to play the original Donkey Kong and Rare's own Jetpac.
Doing enough damage to Ouromov in the "Silo" level causes him to drop his briefcase, although it has no function. At one point, picking it up was meant to be an objective and would have contained plans for either the prototype helicopter or the Goldeneye satellite.
A massive amount of unused items exist in the game code in varying states of completion. Many of them are various gadgets from past Bond films, as well as the exploding pen from the Goldeneye film itself.
Ouromov's car in the "Streets" level was meant to appear in the opening cutscene, as a fully functional model and some pathing code for its AI exist in the files.