Weyland-Yutani Corporation (Alien (film)) - This enormous inter-planetary/multi-national conglomerate, generally referred to as "The Company" (indicating its sheer size and realm of influence), apparently finds it morally acceptable to impregnate its employees with chestbursters, disregarding the very real possibility that a single xenomorph could wipe out the human race, in order to acquire the Alien-DNA for their reverse-engineered biological weapons development.
SPECTRE (James Bond) - This corporation is a global terrorist commercial enterprise that hides its true motives behind seemingly legitimate visage and turns hefty profits by playing both sides of the Cold War. Unlike other corporations, they are fully aware and embrace being an "Evil Corporation" (as evident by their acrconym: SPecial Executive for Counter-intelligence, Terrorism, Revenge and Extortion).
Globex Corporation (The Simpsons) - This corporation only appeared in a single-if memorable-episode. A deliberate parody of "Evil Corporation", the company (owned by Hank Scorpio) at first appears to be one of those "progressive" 1990s workplaces (where the boss wears loafers and everyone is on "flexi-time") until it emerges the loafer-wearing boss is a James Bond-style supervillain hell-bent on destroying the world. All while offering his employees free lunch and messages.
Umbrella Corporation (Resident Evil) - This omnipresent multi-national conglomerate arguably defines "Evil Corporation" and is a text-book example of "corporatocracy gone wrong" and "The Evils of Capitalism". It is an international biochemical and pharmaceutical company portrayed as an international player and the worlds' leading supplier in petroleum, cosmetics, consumer products and foods, pharmaceutical goods and medical supplies, healthcare and health insurance, computer technologies, along with more clandestine operations utilizing military hardware, biological agents and genetic engineering, their legitimate status being only a front for their secret research of bio-organic weapons (which forms the majority of their profits), developed through the use of a unique vector-virus (a powerful mutagen that could dramatically alter living and recently dead organisms) discovered by the company founders shortly after World War II. One of Umbrella's subsidiaries is UBCS (Umbrella Biohazard Countermeasure Service), a private military company with a highly trained security force (composed mostly of convicts, war criminals and exiled soldiers) capable of targeted killing, counterintelligence, rescue and reconnaissance paramilitary operations, "field testing" Umbrella's bio-weapon prototypes, and are even authorized the use of nuclear weapons (as evident in the nuking of Raccoon City after the "zombie outbreak", an event that they directly caused); the corporation used its top-secret special forces group to secure and protect its assets and high profile employees.
VersaLife and Page Industries (Deus Ex) - This corporation manufactured an extremely aggressive nano-mechanical virus with a 100% mortality; which could have destroyed human life on Earth—all in the name of shameless power-grabbing and profiteering.
Abstergo Industries (Assassin's Creed) - This corporation is the public face of the Templars, a monastic military order-turned-corporate giant. Much like the Assassins, the Templars have existed through the entirety of recorded human history. They are a secret society of people whose only goal is "save humanity from itself." To achieve their goal, the Templars plan to obtain the Pieces of Eden, which will allow them to control human minds.
Cobra Industries (G.I. Joe) - This corporation's subsidiaries (such as M.A.R.S. Industries and Extensive Enterprises) are involved in communications, pharmaceuticals, and military technologies. Numerous governments have long suspected them of criminal activity, but has no evidence.