The MGS series as a whole has legendary boss fights. Psycho Mantis in MGS1, Laughing Octopus in MGS4, Solidus Snake in MGS 2, Sahelanthropus in MGS V, and the fight against Liquid Ocelot.

Psycho Mantis and The End, though, have always been the two that stuck out as the most inventive and unique, if not memorable from a story perspective as well.