I don't know if I ever "fear" an enemy in games as a rule. In any game, the key is simply having the proper tools at my disposal to solve the problem. If I don't have the firepower to kill some enemy, or the enemy cannot be killed, my only recourse is to run and try to find an alternative solution. If an enemy excells at close quarters combat and I only have weapons for fighting at range then I simply must find a way to maintain my range advantage.
As such, while there are times where I dread certain encounters, the general trend seems to indicate that I'm fully capable of dealing with the problem.
If it is a question of "enemy type I least like to face" it is probably a "sniper" archetype. People can desperately try to defend their reasons for resorting to the sniper rifle if they want, all I know is snipers are the quickest way to earn my ire.