I think I posted something here before my computer croked...
Anyways, I'd have to say Genobee from Armored Core Nexus. Hes a friggen beast! Normally, he'd be pretty simple, however, he doesn't have to deploy to fire his high power grenades. The reload time on those grenades has no real impact on him either, since he can be flying and firing.
Another boss, or group of them is in Armored Core 3, or Armored Core 2 Another Age. There is one mission where you have to explore some new area. You get 1 easy enemy at first. Then you get another one, then another one, I do believe there are 3 of them. They're only difficult because you don't get repaired or more ammunition through it.
Warhammer Dawn of War... Anything involving 2 squiggoths is hard.