Super Metroid: The final fight against Mother Brain, it was the most amazing thing I'd ever seen in a video game the first time I got there and beat Mother Brain. That moment when the baby Metroid shows up...

Hitler from wolfenstein3d. I thought the level and boss was well designed.

Bowser in Super Mario World.

I liked everything about doom episode 1 final map. You thought you were done after killing the pair of barons of hell and horde of spectres, you thought wrong.

This boss does suffer a problem that many bosses in mario-likes have; you can only hurt the boss when the boss lets you do so. In this case, you need to wait for the boss to throw something that you can use as a weapon, as that is the only way you can hurt this boss.

On the other hand, at least the boss throws weapons out in regular intervals (so the time you have to wait is consistent and reasonably bounded), and the timing to actually get those weapons isn't tight, as they stick around for a bit if not used that way. At least it's not like that one bat boss in Ys 1 (which is bad enough that some players quit playing right there).

I could also say that modern Ys games have some good boss battles, even though I don't like the game changing the rules for boss fights. (Of note, boss fights are one reason why it's best to treat the Ys games as action games rather than RPGs; in an RPG, much of the strategy in boss fights is deciding when it makes sense to heal and to manage your resources; Ys bosses, on the other hand, are more about learning the boss's attack patterns and then dodging them, which is what you would expect in a pure action game.)

(Modern Ys games include the Naphistim engine games (Ark of Naphistim, Oath in Felghana, Ys Origin (that one bat boss makes a return, but is much less painful this time around), and likely includes the more recent games in the series (7, 8, and Memories of Calceta, but I haven't played those).)

Vicar Amelia- Bloodborne

Cursed Amigdala (in the Bloodborne Chalice Dungeon)- took me 4 hours straight to work out how to beat it.

Dancer of the Boreal Valley- Dark Souls 3, gave my Pyromancer a lot of trouble and one of the best animated bosses ever.

Ornstein and Smough- Dark Souls, I'll never forget that epic battle the first time, with help from some random person in Japan, taking turns drawing aggro whilst the other healed.

Hino Enma- Nioh, what sort of developer puts the hardest boss at the end of the first dungeon?

Basically, the only bosses I've ever liked are all in From Software games or Nioh (Team Ninja). I can still remember almost every boss even years later. The types of bosses I hate are the ones that make their difficulty using scripted sequences- the ones where your kicking ass, reduce the boss to zero health (or some fixed amount) and then a cutscene or QTE sequence pops up where the boss recovers and beats on you. I always feel cheated when developers do that. The recent God of War did that- the only bad part (the main battles) of an otherwise great game.

I second that!

The final fight in Hellblade: Senua's Sacrifice is epic in so many (emotional) levels.

The very final boss at Mount Silver in the postgame of the Johto Pokémon games was a genius idea.

Deus Ex - Gunther Hermann. "Laputan machine". If only all boss fights were like this...

Dragon Age Origins - Flemeth. A lot of people found that mid-game battle harder than the end one.

No One Lives Forever 1 & 2 - Inge Wagner and Pierre The Mime King. For the sheer humour.

Pretty much every boss in Metal Gear Solid; great style overall.

Typhon in Titan Quest.

Battlelord in Duke Nukem 3D.

Cheogh and Shial in Blood.

Have you seen that fight in the ACE (Arbitrary Code Execution) speedrun of the game (original GBC versions)?

Fight with Nemesis on the rooftop especially on inferno difficulty where any hit from him could kill you. It was a epic battle with fire all around you.

I haven't. I'll look it up!

It's not going to be what you'd expect.

It might also be worth looking at the glitchless run's version of the fight, if you want a more conventional fight.