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[BanditKing]

Last boss of Bayonetta.

 

[ScrabbleDude]

I haven't read the whole thread, but a couple that must have been mentioned.

Mother Brain from Super Metroid. Amazing fight. Not incredibly difficult, but carried emotional impact.

Gades in Lufia 2. When you defeat him. Not an easy fight, and the first time I saw what happened afterwards I honestly thought I had just beaten the game. If you beat Gades the first time you fight him and are supposed to lose, that's a super hard fight.

 

[Hawkian]

Portal 2!

 

[Freezie KO]

Turtles in Time

Shredder Boss
- Shredder is sitting in this machine as if in a proscenium theatre, while firing lasers at you. He's entirely in the foreground, and as he shoots at you, you have to use the move where you throw foot soldiers at the screen, which crash into Shredder. Memorable.

Gunstar Heroes

Seven Force
- Treasure is known for their bosses, and Seven Force is a perfect example of a boss with many forms. He keeps transforming, each one with unique, fun mechanics. Each time you wonder if you've finally made it out alive.

 

[Uchip]

winner
also OoT's ganon/ganondorf

 

[LuchaShaq]

Basically every boss in Persona 4 was super memorable to me. Especially

Spoiler

Yukkiko/Mitsuro

Strangely enough I remember almost nothing from P3 bosses.

 

[Ether_Snake]

Final Fantasy Tactics/War of the Lions

Belias (forget what he was called in the original). Forced me to restart the game because he was super hard and my characters were unprepared, and I only had one save right before the fight. Finally got to him again, and he was still super hard, but beating him felt so good.

Oh yeah! I almost gave up on him, but finally defeated him with the last possible attack with a cheap summoning spell. If he hadn't died, I would have lost and would have had to start over or something.

 

[Chuck Norris]

Holy chit I can't believe I am the first one to post this SOTC boss:

http://www.youtube.com/watch?v=mPNk1SEbLMQ&hd=1

I loved that boss too, very underrated

I remember being blown away by the effects and motion blur when you jump on the wing. I remember also doing some awesome trick when the bird flipped over and I let go and caught the other wing