E

The Empire - as seen in Elite: Frontier
Allegiances, and associated morality, in the Frontier-verse were always yours to choose, but the Empire’s shameless trade in human slaves tips them clear into the dark side. You join their faction and you’re siding with the extreme right-wing of the galaxy; don’t join them, and you’ll be persecuted by their creepy bone-white ships wherever you go. They’re the Confederates of the game - hateful and arrogant. Ooh, they make our blood boil.

Ethereals - as seen in UFO: Enemy Unknown
The first X-COM did a splendid job of cleverly regurgitating sci-fi tropes to create its alien races, but these creepy, floating robes turned up late in the game and shook our faith in our own abilities. Unnervingly resistant to conventional weaponry and largely attacking with psychic powers rather than the guns of other races, they were the silent masterminds of the alien invasion of Earth. When you finally managed to capture one and dissect it for research, it turned out that, underneath the Jawa chic, it was a spindly pink thing a schoolboy could rough up.

F

The Flood - as seen in Halo and Halo 2
Though this zombie/water balloon hybrid turned up in Halo’s low point, the Library, they very much stuck in the mind. A dramatic change of pace from the smart Covenant, who came at you with guns, swords and grenades, these guys lived up to their name - rushing at you in terrifying massed hordes of shambling monsters and parasitic globes. There just didn’t seem to be enough ammo in the world to take them all down. Surviving them felt like true heroism.

G

The G-Man - as seen in Half-Life, Half-Life 2 and assorted expansions

It’s entirely possibly that the strings Half-Life’s spooky suit is pulling are for the ultimate good of humanity. At the same time, his reality-warping powers and odd speech tics suggests he’s not, himself, human. However, the fact that he keeps at least one person locked in a time-lost cupboard whenever he’s not forcing him to go out and shoot stuff suggests he’s probably not a terribly nice man. Whatever his motivation, the G-Man is an unforgettable icon of PC gaming, menacing despite not looking or acting capable of fighting his way out of a wet paper bag.

The Guardian - as seen in Ultima VII-IX and Ultima Underworld II

The first time the Guardian appeared in Ultima VII, he seemed almost helpful, proclaiming himself protector of the people of Britannia. His true aim is to conquer and corrupt worlds - it’s just that he relies on lies and the help of gullible innocents to do so. Your character, the Avatar, doesn’t actually get to fight the big red muppet until the much-maligned Ultima IX, where he discovers that hitting the Guardian hurts him too, which is annoying. That’s because the Guardian and the Avatar are apparently two halves of the same being, a revelation that upset a lot of dedicated Ultima players, who pointed out that this was wildly inconsistent with what had gone before.