Medusa Heads are incredibly annoying, especially when they're located in areas with spikes (since being hurt in stone form causes double damage... and falling into spikes already deals a lot of pain).
Sea Creepers from Resident Evil: Revelations are annoying as well (unless you have shock grenades). Nothing worse than two Sea Creepers in the same area without a Shock Grenade. Prepare to mash the Y button. 
Chilfos from The Legend of Zelda: Twilight Princess. That room full of them in Yeto's mansion was terrible.








