Daleks- The Emperor came to Skaro and destroyed the city of Kaalaan, where the Kaleds were based. This ignited the war between them and the Thals, leading to the creation of the Daleks.
Madame Kovarian- A disease came to the Gamma Forest and infected its inhabitants. Kovarian was saved from the disease by the Emperor, on the condition that she abduct Melody.
Dark Avengers- The Emperor restored Norman Osborn's sanity, as the Green Goblin persona had left him a virtual sociopath. After leaving him in his office unconscious, he wrote down in front of him: 'The siege has ended, and they have won. Fight back, Norman.' This inspired him to create the Dark Avengers, and eventually, the Dark X-Men.
Cybermen- Mondas was seperated from our solar system by the arrival of the Moon, and its people were beginning to fade. The Emperor gave their council a suit of robotic armour, which they stole and replicated, believing it to be the ultimate form of life. He also returned and showed them the planet Earth, exactly identical to their own, as he knew that this would cause the First Doctor to regenerate from weariness.
Mister Sinister- The Emperor kidnapped Nathaniel Essex and gave him to the Company, who rewarded him with the Vortex Manipulator prototype, which enabled him to return his wife to a semi-human form after the events of X-Men: Mutant God. They eventually gave him his abilities, and the Emperor attempted to fight back with an assembled team of mutants. Because of his telepathic powers, Mister Sinister turned the team against their leader, and eventually made them his own, naming them the Marauders.
Scientists- The planet Nekros was originally barren, until the Emperor came and induced a bio-bomb, creating the ancestors of the Scientists. He also manipulated their genes so as to be what they are today.