This is the first poll where I'd be fine with any of the options (and not only because it's the first poll where I own all the games). I guess I'll go with Perfect Dark though, it's still my favourite Nintendo 64 game, and it could be interesting to talk about what the game meant for its time, and how the genre has evolved from here -- and how it hasn't.
To add a little more about Conker's Bad Fur day, the original N64 game does have some censorship, but the XBox version has more so. In the original, the F-bomb is always censored, and so are some instances of the S-word and a certain C-word. Generally, the one-liners in the multiplayer modes are the ones bleeped out, and the ones in the single-player adventure's cutscenes are not. There's also a scene with male nudity that's pixelated. From what I read, the XBox version censors all instances of the S-word, as well as other words like "twat" and "tagnut," and probably some others. It may also pixelate the scene with female nudity, but I forget. I find a tinge of irony to the XBox version containing more censorship, as historically, Nintendo are the ones who apply censorship to their games.
That's all minor though, the biggest difference is the multiplayer mode. The XBox version has an all-new multiplayer mode, and contains none of the multiplayer content featured in the Nintendo 64 game. It could also be played online, though I have no idea if that's still possible. The final stage of the single-player adventure was also cut from the XBox version, which gives it a different ending.