Here's a list of of video games that were either cancelled, unreleased or heavily reworked into other games that I would like to see their Prototypes/pre-release builds made publicly available on the internet:
Capcom Fighting All-Stars (salvaged as Capcom Fighting Jam/Evolution)
Conker's Quest/Twelve Tales: Conker 64 (reworked into Conker's Bad Fur Day)
Donkey Kong Racing
Dragon King: The Fighting Game (early prototype of Super Smash Bros.)
Grand Theft Auto (Sega Saturn port)
Grand Theft Auto 64 (Nintendo 64 port)
Kirby Bowl 64 (prototype of Kirby Air Ride)
Looney Tunes: Space Race (Nintendo 64 version)
Mega Man Mania/Mega Man Anniversary Collection (Game Boy Advance version)
Mega Man Legends 3
Mega Man Universe
Monica's Castle
Mother 3/Earthbound 64 (Nintendo 64)
Panel de Pon 64 (localized as Pokémon Puzzle League, allegedly included in Nintendo Puzzle Collection)
Project Dream/Dream: Land of Giants (SNES/N64 precursor to Banjo-Kazooie)
Psycho Soldier (Famicom port)
SegaSonic the Hedgehog (Sega 32X port)
Socks the Cat Rocks the Hill (Sega Genesis version, the SNES version is available)
Sonic Riders (Game Boy Advance version)
Super Mario Kart R (pre-release version of Mario Kart 64)
Super Paper Mario (GameCube version)
Ultimate Mortal Kombat 3 (3DO port)
Vic Viper
WWF No Mercy (Game Boy Color version)
Links