Disclaimer
This is a personal list. I have not played every game out there, and a lot of my personal history is Nintendo. I have played several X-Box games and a few number of Playstation games since, but I don't use a game I haven't beaten so no Kingdom Hearts despite playing that game. If your list differs, mention so in the comments.
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WARNING possible spoilers WARNING
You know when the Mario boss ends up last on the list that the list will be pretty good. She is pretty much the boss version of the magikoopas that show up once in a while, and she is fought the same way, by throwing shells at her. Nothing all that impressive but not a bad little boss battle either.
I know Sonic and the Secret Rings sucked, but this game wasn't all that bad. Not great, but fun and playable. The best part of the writing of the game was the big reveal (SPOILERS.... for the rest of the way, ALL but one of these fights are final boss fights)
Still here? Good. Yeah, the girl partner for Sonic turns out to be a traitor and evil, and Sonic, who is the real King Arthur of the realm, turns into a Super Sonic Knight and goes after her in a decent fight. The writing with the plot twist as well as the design of Sonic and the Dark Queen makes this fight worthy. Not the greatest, but not bad.
While I've never did a review for this game, I fell in love with it as a child. While this guy is easy to fight now, he was hard to not only get to at my age (roughly 5) but he seemed invincible. Still now I'm older and this game is far easier. I like the design of the character though and the boss is still challenging and fairly decent fight to this day.
This guy is an example of DLC done correctly. Jyggalag is a powerful deity and is a pretty tough fight. Turns out people didn't like him, and forced him to be the god of madness rather then the god of order, however after fighting him, you defeat him and he doesn't go back to being the god of madness, because you are already taking that spot. This fight is tough as Jyggalag is powerful and likes to shoot lightning out of his free hand. I was trying to summon a small army when I fought him, and he tore through them like butter despite some of them being powerful conjures. A great final boss for the Shivering Isles DLC.
I mentioned her and her fight in Banjo-Tooie as being metal as she has a huge drill machine. This fight is a bit different as she is just a wicked witch with magic. This fight is one of the best boss fights, as you have to use all the skills and moves you've learned, and you still need help from a giant Jinjo like deity to defeat her and send her under a rock.
Wondering if I'd change any list to include an Arkham Knight boss? Maybe I'd put Riddler in the Metal Boss list, but outside of that no. That being said, we still have Arkham City, and Ra's al Ghul is here to use... well magic but actually Batman is tripping out on drugs, but the fight feels like a magic based boss battle so here it is. And it is a pretty fun boss fight as well. This fight does get a little crazy at times.
You won't get away with this Andross... erm wait this isn't a Star Fox villain? Magic!? Jeeze. Anyway, Tiki Tong is stealing bananas from the island Donkey Kong lives on, and making evil tikis out of them. Seems silly until you fight him. He can be fairly grueling in a fight, particularly for your first time. He is a beast and difficult, even knowing how to fight him. Awesome fight though as it doesn't feel cheap.
There are many magic based foes in Legend of Zelda. Heck I was almost going to bring this guy to the party.
but I decided that personally I liked the final fight with Vaati more. It is a three phase fight, and it is fun and difficult all the way through. I liked Vaati's human design, but I didn't get why he was THAT popular until fighting him. I get it now, Vaati is awesome!
While I may prefer other Paper Mario games, I did like this game. The writing behind this game was pretty good, and the reveal that the final boss was a cracked out Luigi was awesome and scary at the same time. Dimentio is an awesome character, and this form of his merged with Luigi was epic. It was a crazy and challenging fight, and well worth any issues I may have had with Super Paper Mario.
Why was Assassin's Creed II so good? Excellent story? Memorable characters? A relatable protagonist? Great gameplay and level design? Maybe it was the final boss which was... the freakin' pope. Ezio was using just as much technology as Borgia was, but still it seemed a lot like magic as there was a great number of glowing assassins and clones of Borgia. The fight was memorable even despite how odd it was to fight a pope, and the story and set up was amazing. Easily one of the best final boss fights of all time, and easily one of the best ones using a type of magic, even if it was technology based.