There are a lot of great boss battles in my entire career, but I usually praise the one that make the fight FEEL like a fair and hard duel between the player and the CPU, such as:
Allen O'Neil -
Metal Slug (ARCADE)
Specifically the Metal Slug 1 variant of this boss (it's recurring during the series) just because it's a pure, simple and deadly fast paced duel between two highly trained (results may vary) soldiers. Allen has one of the best AI's in the entire game, and even then is not frustrating because he's somewhat predictable in his movements. One mistake, and you are done.
I just love this fight.
The other "Allen's Duels" of the latter games aren't bad, but they either add something annoying or unwanted during the duel, just to make it a little more "unfair" sometimes.
Mr.Sandman -
Punch-Out!! (NES)
Alot of people, when talking about Punch-Out!! on the NES, always remember Mike Tyson because... well, it's motherf*cking Mike Tyson, he's the hardest contender in the game.
But Mr.Sandman is special to me. He has close to no unpredictable attacks, and because of that, almost every single hit of his are devastating. Only quick reflexes and a great strategy make this fight winnable.
Plus, he's the only contender in the entire game that doesn't give you any star to perform Star Punches (technically, he does in the 3rd round, but it's still very hard to get them, and in the third round you are pretty much bound to end the battle with a "time up" anyway), making the fight especially difficult, even for experienced players.
No tricks, no easy big damage button: you either win greatly or lose badly.
Traximus -
Teenage Mutant Ninja Turtles 2: Battle Nexus (PS2)
A lot of you are probably like: "what?" and I understand that.
Even tho this game might not be a known as a classic/masterpiece, I can't forget how good it was made under certain circumstances. Traximus' boss fight is another fine example of great duel boss fight. He's invulnerable to thrown weapons (such as shurikens or kunais) so you HAVE to face it head to head with no tricks. His attacks hit as hard as a truck, and most of the times can even stun you if you don't predict them correctly. Parrying his attacks is hard, but if you manage to do so it feels awesome. His AI is pretty advanced too, as it tries to use his strongest attack only when he manages to stun you (I don't know about you, but it feels like an ultimate punishment for not being able to stand up to him correctly).
Just a great fight, maybe not as good as the previous ones, but DEFINITELY deserves recognition from me.
Other possible candidates for great boss fights are:
Gorgon from
Starfox 64
Javier Jaguar from
Guacamelee
Metal Gear Rex from
Metal Gear Solid
Captain from Nuclear Throne
Necromancer from
Castle Crashers
Satan from
The Binding of Isaac