Seven Force from Gunstar Heroes (the boss randomly changes to another form, all superbly animated) :
Guardian Dragon from Panzer Dragoon Zwei :
Shining Force III Colossus battle :
You have to open a dam with a second time, so that the water flows through the bridge, while the first team has to endure the attacks of the colossus, and eventually hides itself between the walls to not be taken away by the water. Great fight.
One of the most memorable, anyway. All of the characters and story came together in ways you could identify with. His relationship to Ramza was tragic, and his end was heartbreaking, even after all he had done.
Back long ago in Everquest there was The Sleeper...a great dragon that was unbeatable. If a guild woke the sleeper on the server...she would leave and.....there were items on that server that you could never get again.
Well one day .. years later...some guilds, a few hundred people got together to kill the unkillable and threw their corpses at it...and accomplished it.
Keep in mind this was back when dieing meant corpse runs and all your gear sat on your corpse.....also you could delevel. many people deleveled by 10 levels or so that day.
The best Metal Gear ones were already named, but I also love the fight against "The Boss". Especially due to the sound design and song implementation.
Shoutout to Hades from God of War 3, which was one of the most beautiful things I had seen in games up to that point. Most God of War boss fights deserve mentioning, as well as Kojima's. And Shadow of the Colossus is tailor made for this discussion.
But alas, let us not forget the excellent boss fights of Ninja Gaiden: Black. In fact, some of the regular enemies are as memorable as some of the best boss fights in videogames. Evil Ryu, anyone?
Great question... Jee... I kind of like how Dagoth'Ur was just another dude standing in a room in the middle of vvanderfell... I also liked the first boss in human revolution after they patched in the non lethal option.. killing him the first time felt great, Owning him the second time felt awesome.. i know, weird reasons.. i can't really think of anything better.. i liked fighting really tough beasts in Witcher 3.