Bloodsuckers from Shadow of Chernobyl are horrible, less horrible in clear sky.
Omega pirate from metroid prime was a damn tank.
Sephiroth (hope I spelled right) from kingdom hearts. That guy was so deadly it was unreal.
The water wraith from Pikmin. Actually that was not the most deadly Pikmin 2 boss, that bloody machine gun spider thing was by far the most deadly, but water wraith was terrifying.
The grox from spore, if only because trying to remove them would take about a year.
Death claws from fallout 3 were deadly in just about every way.