Acclaimed Flop: Though it received positive reviews and has become a Cult Classic, the game did not sell well at all (less than 30,000 units), due to Nintendo refusing to promote the game on top of its coming out at the very end of the Nintendo 64's life cycle when people were more focused on the already-released PlayStation 2 and the upcoming GameCube and Xbox.
Despite refusing to promote the game, Nintendo was actually very hands off with it—Chris Seavor said the original game is 99% intact in terms of content. The only edicts Nintendo gave were to remove or edit a handful of scenes;
The scene in "Barn Boys" after Conker frees Franky originally had a throwaway gag that took a potshot at the Ku Klux Klan. The final game had the reference replaced with the paint pot and brush wearing generic executioner hoods instead.
"Its War" had three scenes edited; originally, Rodent was accompanied by two soldiers who are killed by firing squad (Rodent is alone in the final game—amusingly, this bit was reinstated for Live & Reloaded), a brief scene where a Tediz stand-in for Hitler appeared was cut, and a horrifying scene where a live squirrel soldier is dissected by the Tediz was replaced by a scene of two Tediz chit chatting, using audio that was originally meant for scrapped outtakes in the credits).
The main reason why Conker's Bad Fur Day was created was because the executives at Rare began to fear that their original idea for a Conker platformer, Twelve Tales: Conker 64/Conker's Quest, was going to be looked down upon due to being yet another cutesy platformer, and an extremely negative critique/mockery made during its test showing ended up being the last straw, ultimately resulting in this.
Microsoft made Rare censor the remake, despite the fact that it was an M-Rated game on a console targeted mostly at teenagers and young adults (and despite initial claims that it'd be uncensored, it was originally called Conker: Live and Uncut after all). The reason was because Microsoft wanted the game to be sold at big retail stores, many of who would have refused to carry the game if it was released uncensored.
Averted with the Rare Replay port. The game is almost completely unaltered, apart from editing out the bootup cutscene (due to the Nintendo 64 logo), and acknowledging the new button prompts on the Xbox One (although Conker does originally refer to the original Nintendo 64 control scheme in the voice acting).
Keep Circulating the Tapes: The original N64 version was stuck in this for years. While the Xbox remake came out in 2005, and was easier to get a hold of, it's widely considered to be the inferior version. Fortunately, the original N64 version was put into Rare Replay with almost no changes. This had the side effect of switching positions with the Xbox remake, making that version the harder one to get.
Reality Subtext: The reason Conker is the only red squirrel you see in the game (every other squirrel is gray) is a commentary on how gray squirrels were introduced to Britain and have caused their native red squirrels to become an Endangered Species.
Screwed by the Network: When Nintendo discovered Rare's provocative change in direction, they refused to acknowledge the game's existence in Nintendo Power (though not in their foreign associated magazines from Mexico or Brazil) and other media outlets, contributing heavily to the game's low sales. Not helping was that big retailers like KB Toys refused to stock it because they were worried it would be confused for a childrens game.
Stillborn Franchise: The Conker series has become this after only two titles and some minor cameos in other Microsoft properties, notably Project Spark (which itself had all further support ended in 2015).
Talking to Himself: Chris Seavor does 99% of the voices, with Louise Ridgeway voicing Berri and a few of the incidental female characters, and Chris Marlow voicing The Great Mighty Poo.
Throw It In!: The scene in "Its War" where the two Tediz doctors are talking out of character was originally meant to be a joke outtake used for the games credits, but when the original scene before it, which showed the Tediz dissecting a live squirrel, was ordered to be edited out, the outtake was used in its place instead.
Urban Legend of Zelda: Rumor has it that the developers had planned an ending where Conker, who is depressed over his current dilemma and Berri's death, commits suicide via a gunshot to the head. This ending was supposedly changed because Rare and Chris Seavor wanted to be able to make a sequel to the game and scrapped this ending because it didn't leave room for one. However, there isn't any evidence or mentioning of such an ending existing at all.
An interview with Chris Seavor revealed that not only did they plan on making a sequel to Conker's Bad Fur Day, aptly named Conker's Other Bad Fur Day, but the plotline of the game was actually finalized. However, Microsoft decided against doing a sequel until they decide to ask, so development was shelved. The only known parts of the plot revealed to the public was in the beginning, where Conker was dethroned, imprisoned, and awaiting execution because he wasted the entire royal treasury on beer, parties, and hookers. He then has to make an escape from the castle's highest tower with a ball and chain attached to his leg.
The game was originally a more kid-friendly platformer in the vein of Banjo-Kazooie. At first it was Conker's Quest (which followed Conker and Berri, as they set out to collect a hundred house-warming gifts that had been stolen by magical beings called "The Hoodlums") before changing into Twelve Tales. This younger version of Conker can be seen in Diddy Kong Racing, and the Game Boy Color game Pocket Tales; some Posters released for the remake of Bad Fur Day says both are canon and take place in the past. You can view 30 minutes of gameplay in this unreleased game here.
As seen in this video, there was originally a scene where two Tediz surgeons are experimenting on a squirrel soldier while he's still alive not unlike the Nazi experiments during the Holocaust. It was replaced with the Tediz Breaking the Fourth Wall by talking about the game before turning their attention to Conker. In turn, the replacement scene was originally going to be part of an outtake reel planned for the credits.