Metroid
(not a poll because there are too many cool enemies) 
Probly either Quadraxis or … uh …
Well when it comes to bosses I will have to go with Quadraxis. Just the coolest looking thing ever! Ridley on X is cool too though.
When it comes to enemies, smaller ones … I love metroids. I love the way they look. But … they can get really annoying in game. So I am gonna have to go with the red Clawflyers in Metroid Fusion, the ones that live in PYR and fly around and scratch at you. Pretty aggressive creatures.
Edit :: Didnt notice it said NOT bosses, lol.
Um…Space…Pirates? >_> <_< hides the gun being pointed at head by Daz Hehe…heh.
Yeah, I was going to mention that.
We have a topic for this already.