55. Bob The Goldfish - Earthworm Jim
Bob isn't a particularly threatening villain, with his boss battle's usually ending in Jim simply knocking his bowl over or eating him. However, most of his bidding was carried out by his large, bulky, feline subordinates, especially Number Four who would usually be tasked with carrying Bob's bowl around. If nothing else, you've got to respect him for trying to take over the world all by himself when he's just a little goldfish.
54. The Flood - Halo
The Flood make it into this greatest villains list because of the shock factor that their appearance brought with it. They are a race of parasitic life forms that are driven to infect all living life they come across, something which scared the ancient Forerunners to such an extent that they believed the only way to stop the Flood was to kill themselves by activating the Halo network, effectively starving them to death.
53. Vayne Carudas Solidor - Final Fantasy XII
Vayne is the third son of Archadia's Emperor and a devious politician, who has previously killed his two elder brothers at the behest of his father, before even killing his father to assume his place as the new emperor. He planned to become an all-powerful Dynast King and conquer all of Ivalice using manufactured nethicite, inciting a war between Archadia and a resistance faction towards the end of the game.
52. Big Smoke - Grand Theft Auto: San Andreas
Big Smoke was one of Carl Johnson's best friends and a high-ranking member of the Grove Street families when San Andreas kicked off, although later in the game it was revealed that he had become the biggest criminal, and drug lord, in Los Santos after joining forces with numerous other gangs, as well as Officer Tenpenny. Smoke betrayed Carl and the Grove Street Families just so people would remember his name. Nice guy.
51. Wolf O'Donnell - Star Fox
Wolf is the leader of the Star Wolf team and the nemesis of Fox McCloud and the Star Fox team, after he was believed to be involved in the death of Fox's father. Later in the series Wolf saves Fox's life numerous times, but during Lylat Wars he is merciless and cunning, wanting nothing more than to destroy Fox which leads to some of gaming's most exhilarating and challenging dogfights.