The references are as follows (please list them in chapter order):
It wouldn't be a game by Rare unless there were shout outs to some of their other game franchises; during the main menu Banjo's head can be seen mounted on the wall over the fireplace in the bar, and Kazooie's head can be seen on the handle of an umbrella in the closet where the chapter select is.
Also, like the main page says, one idle animation has Conker pull out a Game Boy Color and play Killer Instinct on it (though Live & Reloaded replaced it with a made-up XBOX handheld that slightly resembles a GBA SP for obvious reasons.).
The Live & Reloaded version added a shout out to Grabbed by the Ghoulies in the menu: you can see Cooper vomiting in a toilet in the save file 3 select section. Also Live & Reloaded has a few shout outs to its N64 counterpart. During the Hangover Chapter if you look around closely you can find Conker's old N64 War chapter helmet (since he gets an entirely new war costume and helmet in that chapter in Live & Reloaded), And in Windy in Live & Reloaded you can see a tree that shows its time rings that counts how many years it's been between the N64 version of the game and the XBOX remake.
The opening to the game is a reference to the opening of A Clockwork Orange, with Conker narrating, holding milk in his hand, and with the same music from said scene (though Live & Reloaded replaced the milk glass with a goblet making the reference to the scene a little odd).
Conker's conversation with Mister Barrel at the windmill about "wanting to go for a ride" is based on an exchange between Frank and Jeffrey from Blue Velvet.
The Haybot boss in the Barn Boys chapter is a parody of the Terminator.
Jack the metal box speaks in a manner similar to Foghorn Leghorn of Looney Tunes fame.
The Bulldog Shark parodies the shark from Jaws, and the scene where the Catfish are killed and Conker runs up a pier to escape from the Bulldog are taken right from the movie.
When Conker first throws sentient sweet corn to the Great Mighty Poo it mirrors a scene from Jaws.
During The Great Mighty Poo's song, a back and forth between Conker and the Great Mighty Poo ("My butt!" "Your butt?") may have been a nod to the Bugs Bunny short What's Opera, Doc?, where Bugs and Elmer have a similar exchange mid-song about his "spear and magic helmet".
Greg the Grim Reaper seems to be the polar opposite of Discworld's Death. Whereas the latter is portrayed as a deep-voiced, tall and imposing figure with a fondness of cats, Greg's a squeaky-voiced midget that hates those bloody critters with an undying bloody passion (but hates The Undead even more).
The boat scene during the War chapter where the Squirrel Soldiers are being slaughtered on the beach by the Tediz, almost mirrors the D-Day scene from Saving Private Ryan (or at least as close as Rare could get what with the graphical limits of the N64).
One of the scenes in the chapter select spoofs Saving Private Ryan's title as the scene is called Saving Private Rodent
In the Casualty Department, Conker finds two surgeon tediz having a "philosophical" conversation about the nature of the game ("What if you were to give this game to - say - twenty intelligent people? I mean, what would that do? Let's face it, what would that do?" "Really, that's interesting") until they notice the red squirrel and decide to "get into character", i.e growling incoherently and trying to stab him to death with flying scalpels.
When Conker and Berri first meet the Panther King the shutters behind him open much like the ones that do in a scene from The Empire Strikes Back.
The final boss is a reference to Alien; in fact Conker repeats the "Get away from her you bitch!" line from Aliens. It's also fought in a similar way to the Bowser boss fights in Super Mario 64, where you have to pick the Alien up by the Tail and spin them around, then let go to try and throw him out the airlock.