The (allegedly cute, bird-like) Guts aliens with their deep voices, ghostly appearance (at least inside their space vessels) in "Seven Assassination Scheme", and for that part, their plan (capture and execute Seven) and tactics (appear and disappear out of nowhere, accost Dan to make him transform and fight, wear Ultra Seven down, crucify him, execute him in front of the whole world) are disturbing to this day.
Then there's that gas-guzzling... thing from "Space Prisoner 303"... the feral Alien Icarus from "The Strange Neighbor"... the faceless dudes from "The Fugitive Fortune Teller"... Perolinga, the inside-out chicken alien thing in "Flying Saucers Have Arrived"... Alien Wild in "Fly to the Mountain of Evil"... Alien Spehl from Episode 12 (a mummy-like creature with glowing welts, a deep voice, and an even deeper growl), especially as it emerged from his hideout, scaring children who had been lured there with the promise of a prize...
For women tropers: If you knew what was hiding inside an unsuspecting girl's body, you'll never smell a flower up close again. Amagi's fiancée found out the hard way in Ep. 31 "The Flower Where the Devil Dwells".
On that same note, women were dying to own the latest Japanese watch, literally... Aliens were feeding off their blood, that is, until their attention turned to children. By the way, this happened in Episode 12, featuring Alien Spehl.
From "The Green Terror": Imagine you turn into a plant against your will, then go on killing rampages across the neighborhood. Now picture your spouse and you going on a vacation trip by train and that happens to you, right in front of all the passengers.
The Ghos aliens' plan to force earthlings to live underground as slaves in Mars (or here on Earth) after destroying the surface, beginning with Paris, London, New York, and Tokyo.