Hmm... from the recent Mortal Kombat, there's Shao Khan (I think that's how it's spelled), otherwise known as one of the most broken characters I've ever played against. Seriously, he can cancel out any knocking-down moves he likes, has a projectile that will always hit and stun unless you jump forward at the perfect time or teleport, and is much more resistant to damage. Not to mention the damage he does is just wrong. Seriously, my Xray attack did 13% health damage to him. His did 51%. This is much less then fair.
Also, any double-teams in the story mode MK9. It's really annoying to face two at once with only one health bar while they have two.
The giant dragon at the end of the third disk or so of FF9. It's the main reason I've never beaten that game. It was insanely powerful and made me want to kick a baby.
The cazadors from Fallout: New Vegas, as they were very overpowered.
The creepy zombie-things from OoT, for scaring me as a child.
Most of the enemies in Halo: Reach on Legendary for being very overpowered.
Every enemy from CoD: WaW, for having infinite respawn abilities and killing me with four or five shots, if I was lucky.
And finally, the last one I can remember, the zombonis from Plants Vs. Zombies. Those things were very annoying and would normally get pretty far if I wasn't ready for them.
I know there are more, but those are the ones that pop up off the top of my head.