The last boss battle that I've done was Megaman Zero 2's Phoenix Magnion, and after 100 tries I've finally beaten the fireball.
Last boss of main story mode of Digimon Story Cyber Sleuth: Hacker's Memory. ...Probably can't mention it for spoiler reasons.
Not sure if this would be considered a boss, but the Alien from Alien: Isolation... man, that thing is terrifying.
Do "outlaw" battles in Super Mystery Dungeon count? Because oh my god, why do they make it so the only mission you're guaranteed to have access to as your third mission is a battle against a SALAMENCE? Axew didn't even need our help as far as fighting. I just used wands to give it the truant ability and keep it asleep and confused at all times. It still managed to get a lucky hit off and knock out one of my team members, which is more than I can say for any of the actual bosses in the game so far.
I'm pretty sure it was Orochi in Okami HD. But I haven't played video games in a while so I could be wrong about that.
EX Sphere Doomer in Kirby's Return to Dream Land. Wasn't that hard off a boss thanks to me using Spark. (That ability is so good in this game! Glad you only have to shake the Wiimote to get a full charge.)
Calamity Ganon in Breath of the Wild, which turned out to be a lot different than what I was expecting.
Super Mario Odyssey’s ending boss. That end, with that (spoil) + - new song and that twist... It was just perfect!
Nanimon on Digimon World Dusk. He was pretty hard, at level 24 while my team was around 16-21. I nearly lost, and my team was doing little damage. Managed to get a few levels off of him, though.
Does the "final boss" of an Ace Attorney game count? Because the last game I beat that has a 'final boss' of any capacity would be Miles Edgeworth Investigations 2: Prosecutor's Path. And yoooooooooo those twists at the end are mind-blowing.