4) Metroid Prime
Featured In: Well, Metroid Prime (2001)
The titular character for the original GameCube classic lands in at #4. Metroid Prime remains unseen throughout the game literally until the end, but its influence can be seen throughout planet Tallon IV.
The source of this Poison was a creature they referred to as "The Worm". Conflicting sources imply that somehow the Space Pirates encountered this beast, but it doesn't make sense considering the intricate seal placed on the Impact Crater. Once you've gathered all the necessary artifacts to gain access, you enter the lair of Metroid Prime.
This battle has two phases, one against the creature's exoskeleton and the second it's core form. During the former, Metroid Prime utilizes ultrafrigid breath, a missile-like launcher system, and a Grapple Beam. Its appearance changes color throughout the battle to show what weapon it is weak to, allowing you to blast it in the face with some cool beam combos.
Eventually the core form busts out and faces you. This form creates Metroids to keep you occupied and in the process generates a pool of Phazon. This proves to be its undoing, as you can stand in the Phazon and power up your beam to seriously damage it.
In the end Metroid Prime dissolves into a blob of Phazon, and attempts to pull Samus into it. It yanks the Phazon armor right off of her, leaving her in the previous Gravity Suit. Samus then escapes the Crater, but a armor clad hand rises out of the pool of Phazon...
4) Phantoon (Super Metroid)
Phantoon is a fight with a ghost. What's not cool about that? Especially a ghost that looks like an octopus, and shoots fire balls at you. I love trying to dodge those blue fire balls while waiting for Phantoon to open that eye that you can shoot. I enjoy this fight a lot, and that's why it's number 4.