Some of the most memorable characters in modern video games do not have a face. Some of them may have a logo, although this is not always the case. Video game developers understand something H.P. Lovecraft understood when he wrote his articles in the twenties and thirties. The most threatening villains often do not have a face, and they treat people like things.
Cloud and his companions battle the Shinra Corporation. This corporation, which rules the Final Fantasy VII world pursues its agenda without regard to its consequences. Its production of Mako energy threatens the world. Some of its side projects, like Sephiroth, pursue their own dangerous agenda. Ultimately, Shinra isn't evil. It is more accurately described as immoral.
Valve may not be able to count to three, but the workers of Black Mesa are more than capable of battling alien invasions. Gordon Freeman earns his pay check in the first game. It is hard to judge Black Mesa's intent, as they did not intend to allow the aliens to invade the earth.
Aperture Science teaches us that we must be responsible with our creations. Much like Doctor Frankenstein, the company's researchers push science to its end. The trend goes all the way to the top. Even the founder produces combustible lemons.
Aperture Scientists start out with good intention, but they let their creations go well beyond their control GladOS's use of a deadly neurotoxin on Take Your Daughter to Work Day serves as a warning to us all.
The Umbrella Corporation
When it comes to being the pinnacle of Evil, Capcom's Umbrella Corporation may overthrow the Lord of Darkness himself. The corporation has no qualms about experimenting on unsuspecting populations.
Many Resident Evil games feature a protagonist who finds out about one of the corporation's more infamous hives. The company attempts to seal off the hives in order to prevent the plagues they unleash from spreading.