So, we're talking about normal enemies, not bosses, right ? So, my top five would be, in no particular order :
1) Caliban (Silent Hill Origins ):
Very creepy, especially the way they stand, they walk on four legs, but their back legs are bent in front of their body, if that makes sense. Can you picture it ? They are first introduced as bosses, but they return afterwards as normal enemies with slightly less health. Really tough opponents, fighting them is unwise. If you see one, just run.
2) Samurai Wasp (Alice Madness Returns)
They offer a decent challenge, and I always found them cute with their samurai armors.
3) Protectors (Bioshock/Bioshock 2).
I don't like their English names. They are called Big Daddies in the English version (although they are referred to as Protectors in some audio logs) and the little sisters call them Dad ( I think). In the French version, they are called Protectors and the Little Sisters call them Mr.P.
4) Stage 3 Mutant (Obscure/ Obscure 2 )
Not expecting anyone to know this as this is an obscure game (LOL) and not very well known outside of France. Since it is a French game by a French studio. Introduced via a cutscene in the late game, they are really tough and just plain scary with their one-hit kill.
5) Assassin (Wolfenstein)
The Nazi Assassin, one of the most powerful soldiers in the Wehrmacht. Has the ability to become invisible for a period of time and even to teleport behind you. Is armed with two knives and loves to kill people (civilians and enemy soldiers alike). Oh, and the substance that allows him to become invisible also alters his mental abilities, turns him crazy. That's why he is such a cold blooded killing machine.