Metroid Prime 2 is noticeably absent from this discussion. The Torvus Bog boss (the giant insect in the poison pool), Emperor Ing, and Dark Samus all rank high IMO.
MGS is loaded with great bosses as well. Sniper Wolf would probably be my favorite from a gameplay standpoint. The Boss from a story/emotion standpoint.
The Elevator Crab fight from Castlevania: Order of Ecclesia has stuck with me for well over a decade. Easily one of the best Vania bosses from a gameplay standpoint. Props to Legion in SotN for the WTF factor.
Ghot from Majora's Mask is fun and unique because of the Goron gimmick.
RE7's Garage Fight and Chainsaw Fight were insanely fun (though admittedly clunky). RE3 Remake battle with Nemesis on the rooftop was epic (assuming you played on Hard mode)
malyg posted...
No MGR probably has the best ever first boss battle tho.
Castlevania: Lords of Shadow has an amazing intro fight as well. Early 2010s Konami had that down pat.