Honorable Mentions:
Union Aerospace Corporation (Doom). While not inherently evil — at least no explicitly so in the games — the UAC is responsible for the opening of a portal to Hell on one of their Mars research station that resulted in the legions of Hell being let loose into our world followed by the violent deaths of nearly every living soul on the outpost.
Tricell (Resident Evil 5). While not as bad as the Umbrella Corporation, Tricell was behind the Plaga outbreak in the African town of Kijuju. They put my man Chris through even more awful crap and ruined Albert Wesker. They suck too.
