I always like the "boss-fight" enemies that weren't actually bosses.
Playing cat and mouse with a Gargantua in Half-Life
The David vs Goliath battle of fighting a Tank in L4D. (presumably while it's being controlled by a competent human)
Trying to take down an Assault class 'Mech with a group of scout 'Mechs. (in any MechWarrior, MechAssault, or MechCommander game)
Pushing back a horde of Ultralisks or Carriers using nothing more than Marines and Medics.
Essentially, what I'm saying is, I've always preferred enemies that pose a significant threat and require creative thinking, adaptability, and lightning quick reflexes. Ones that, if you falter even the slightest, result in a "game over" kind of situation.
Though, my single favorite "enemy" in any game from any time would undoubtedly have to be GLaDOS. She promised me cake. Put me through hell to get it. Then took it away. So I killed her. However, she had the audacity to survive.