Final boss of Rune Factory 3 (forget its name... very fun and difficult... best action RPG boss I've ever faced, with such an epic and on-edge ending to the battle!)
Pyscho Mantis from MGS1. I think he illustrates the brilliance of that game well.
The boss where you pull the chains in Twilight Princess (sorry I'm bad at names haha). Even though it was easy and people can call the bosses in that game "gimmicky" they had such a fun FEEL to them. It just felt great to defeat them. I didn't even care it was easy even though I normally like difficult games.
Chaos from UNLIMITED:Saga. Just for being the most difficult RPG battle I've ever faced in my life.
Commando Man from Mega Man 10 (hard mode!) ... This is the perfect platformer boss difficulty. I can't even express how excited I was to no-damage him for the first time :) Plus he looks really cool.
1. Mr. Freeze - Batman Arkham City 2. Psycho Mantis - Metal Gear Solid 3. Colossus #13 - Shadow of the Colossus 4. Courtney Gears - Ratchet and Clank: Up Your Arsenal 5. Mz. Ruby - Sly Cooper and the Thievius Raccoonus
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