Games with Amazing Boss Battles
Games with at least one boss that, for whatever reason, stood out to me as a highlight, regardless of quality of the rest of the game. Spoilers ahoy, by the way.
77 Games
Various
Giegue
Draygon, Ridley, Mother Brain
Kefka
Giygas
Odio (The remake too, and it in fact makes the final boss better, but I'm only listing the OG)
Magus, Lavos
Kaptain K. Rool
Jenova (Various), Sephiroth
U.B.
Gruntilda
Psycho Mantis, Liquid Snake/REX, Revolver Ocelot, Vulcan Raven, Sniper Wolf... like all of them lol
(G/S/C/HG/SS) Red
The Transcendent One (More if you choose to debate it out with him rather than actually fight)
Miracle Matter, 02
Biolizard
Nelo Angelo
Solidus Snake
Pious Augustus
Metroid Prime
Matador, Dante, Kagutsuchi, Lucifer (Arguably plenty of others too)
Miror B <3
Quadraxis, Dark Samus 3, Emperor Ing
Like, actually basically all of them. The Boss, The End, Ocelot, Volgin, The Sorrow... even the less memorable ones like The Fear/Pain/Fury are pretty great.
Verdugo, Krauser
Cerberus, Agni & Rudra, Vergil (All three times)
I'd say literally every boss in this game is amazing or awful with little in-between, but I'm going to cite Malus, the final boss, as the best one.
Elder Princess Shroob
Ninetails, arguably Orochi and Yami too, but Orochi is overused and kinda lame and Yami never really hit me very hard.
Uncle Rupee
Elvis (All three), Azel (Both)
Rundas, Mogenar, Omega Ridley
Glados
Half the bosses in this game qualify but Jeane and Henry above all others.
Credo, Dante
The Queen
Assassin Asha, Annihilator Iosa, General Tor
Giratina, Cynthia
Dark Bowser
Jeane, Father Balder
Margaret Moonlight, Vladimir
(B2/W2) N + Ghetsis
Wheatley
Knight Artorias, Orstein & Smough and Gwyn, Lord of Cinder
(B2/W2) Ghetsis
Rebel Flagship
Bladewolf, Monsoon, Sundowner, Jetstream Sam, Senator Armstrong
Ouroboros (I think Serpent Eating The Ground might genuinely just be my #1 final boss theme and I don't even like BD that much)
Sectonia
I don't wanna go through the five different games so I'm just gonna say "a lot of them"
Heart of Darkness
Daisaku Kuze (You fight him like 40 times and all of them are great), Keiji Shibusawa, Lao Gui, and likely several others I forgot.
Papyrus, Asgore, Flowey, Asriel, Sans
Goro Majima, Akira Nishiyama
Krishna, YHVH
Final Boss
Star Dream
Kinda all of them (save for The Flame, he's boring) but especially The Edge
Grimm/Nightmare King Grimm, Dung Defender, Hornet, Hollow Knight/Pure Vessel, Radiance, Mantis Lords
Proteus Ridley (Begrudgingly), others
I can't quite pick out someone that stood out above and beyond all the others but the quality is so high overall that most would make it here.
(US/UM) - Ultra Necrozma
Part Of Me
... Hades
Nyarlathotep
Electro Triple Star, Brian Buster Jr, Smoking King, Eight Hearts, White Sheepman, Silver Face
Vergil (Who appears 5 times in this list LOL)
Psychiatrist
Gabriel (Both times). I haven't gotten to either of the Primes yet.
Mother, Dogma
Lord of Doors
Raven Beak (as well as others)
Kale Vandelay, Rekka, Roquefort
Jevil, Spamton NEO, The Queen, The King