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The Comms Officer/Scagdead and Undead Rachel are the only enemies in the game that make you curse and go on the defensive. So they win as best enemies. 3rd place goes to the rock dudes that when you break them, have a second form of either crawling or running around zapping you. (Forgot the name) then the BIG rock dudes (Though I hate their smaller forms more) and lastly the Hunters.
Out of the list, it would have to be the Scagdead, although I do love the Scarmiglione because you get to blow the head or legs off. However out of every enemy in the game it would have to be Rachel thanks to her brilliant voice and script, plus seeing her die right at the beginning of the game was so atmospheric.