Prior to their identification, the Novans, although Human, were called alien by Captain Jonathan Archer, and later, the Takret were called alien by T'Pol. (ENT: "Terra Nova", "The Catwalk") The 22nd century inhabitants of Earth referred to the Borg as aliens, as the species was unknown at the time. (ENT: "Regeneration")
In the first draft script of ENT: "Fusion" (which had the working title "Equilibrium"), Trip Tucker mentioned to Fraht that, for Halloween during Tucker's childhood, he had usually dressed up as either an alien or an astronaut. Fraht, having been wondering what to wear for an upcoming Halloween party aboard Enterprise NX-01, reasoned that, among Humans, he actually was an alien, so Tucker advised him to attend the party just as he was.
A deleted scene from TOS: "Return to Tomorrow" had Spock compare sharing his consciousness with Christine Chapel, a woman, to being in the mind of an alien. Ann Mulhall, amused, then referred to Chapel as her fellow alien (female). (Star Trek: Lost Scenes, pp. 191-192)
In Star Trek Online, "Alien" is used to refer to a playable species for all factions except TOS Starfleet and the Dominion. Alien players receive no special traits, but instead can choose additional traits from the shared list. Aliens come with an enormous degree of visual customization, and it is possible to customize an alien officer's appearance to match some of the less common species seen in Star Trek, or create something entirely new. It is also possible to recruit alien bridge offers with randomized appearances.