Ah, too much like Pringles! Can't choose just one. I'll keep it short, though. Oh and don't forget the
spoilers! I'm gona explain why I like 'em, so that'll
ruin things for you if you haven't played 'em.
In no particular order:
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Final Fight With Gannon in LoZ: Wind Waker: OH MAN. Not only did I just love Wind Waker's battle system (the button presses make it so much fun) but that mixed with the final boss made for a real epic fight. It was tough, but fun, and ended in the most spectacular fashion of jamming the Master Sword into Gannon's skull. Just awesome.
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Bydo Core in R-Type III: You've already gone through hell in this game, trust me. HELL. That's not even counting the final level that leads up to this horror. It's mass of green fleshy madness with many arms and a head that you have to blow off more than once
to even hit it. After what feels like forever, the thing finally blows up, only to leave the severed arms to spin and attack you as the Bydo dimension rips open and deposits you back into space. You're safe! But wait...NO. The friggin' Bydo Core
holds the dimension open with it's arms and tries to shoot at you. Your only option? Launch your Force (weapon pod) backward right into it's face! NOW you're done! Awesome, terrifying, EPIC battle. I love it.
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Sigma in Mega Man X4: Just all around fun. Keeps you on your toes and never lets up. All his forms keep you jumping and tapping those buttons, though my favorite part is his crazy ending where he's got multiple forms at the same time! He switches between them while you fight them to
pounding metal music and rush back and forth trying not to die. I will admit that the music is what pumps me the most, but the boss is still fun in itself.
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Craft in Mega Man Zero 4: Most of the time, when you fight a regular dude in a side scroller, it's not too hard. They're small, they have simple attacks, and thier only useful tactic is speed. Craft, though...man. This guy is ready for everything! He's got a way to counteract every motion you make, and if you try to stand there you're a murdered pile in two seconds. He's the ultimate in speed when it comes to side scrolling action. Just keep it up! If you don't: he WILL.
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Mother Brain in Super Metroid: I've played it so many times that it can't possibly be hard anymore, but I still love it. The first fight is classic fun, then the banging, dark music starts and she rises from the ground with some horrible bio-organic body. It's a tough fight (back in the day) and it ends in that classic epic scene where the baby metroid gives you it's power in it's dying "breath" (if they breath). Then you blast the ever-loving hell outa her face and do your Metroid "RUN AWAY" to the ending of the game. One of the best!
Alright alright, I've said enough.