It's late, I've had about 2 hours of sleep and have been hit upside the damn head too much, so here's my two cents...
1) Manfred Von Karma during both of the Edgeworth Trials (Phoenix Wright: Ace Attorney...let's just say that dirty rat bastard objects you on everything.)
2) Jet Stingray (fighting as Zero, MMX4) because the damn game doesn't let you hit the ice attack at a high enough distance, and so you end up getting nailed.
3) The Forgotten One (Castlevania: Lament of Innocence for PS2)
4) The First Boss from Ninja Gaiden Black for XBox. That bastard kicked my ass, every time. Still does. I can block about 2 attacks, he looks like he's going to chain the attacks, and then...I get thrown halfway across Wabashaw.
5) Cerberus from Devil May Cry 3. Anyone say bad dog? (Especially hard w/o use of the Devil Trigger.)
6) The Weapons from FF7. It's a royal pain in the ass to prepare to fight them, and what's worse is that when you get there, they slap you around something fierce.
7) Crow from Def Jam: Fight For NY. The guy was a grappling bastard, I'll give him that.
Dauragon C. Mikado (3rd Form) from the Bouncer. By this point, you've got no health, no defense, and your fingers are aching like a madman.
9) Sphinx (Rygar: Legendary Adventure) because of those damn homing fireballs.
10) Magus from Chrono Trigger. Sassarassafrassin barriers...grr...guy had me deadlocked in a battle for 2 straight hours.
