Alien (1979) is the most alien alien ever. She was intellient, while slightly humanoid in appearance was still just NOT human at all, but still has that whole motherly instinct....Well, until ripley beat her up and then they made the last few sequels which were the devil.
Anyways...
Another alien I have always had a soft spot for is the tribbles (star trek). Seriously, has there ever been a cuter alien ever? And space herpes from ice pirates, they just cracked me up, although those might not actually qualify as an alien.
Oh, and don't forget The Blob (1958 not the crap remakes or spin offs) there is an alien that has absolutely NO form, NO thought other than to consume....us....
And then there is The Thing (1989), which is supposed to be 'alien' but I never really thought of it as an 'alien' but more of a primordial monster living in the ice like on x-files.......but since the thing was formless and only assumed forms, changing it and destroying and stuff.....
And then, lets not forget It Came From Outer Space (1953) because that was just a ship that infected/changed people and you never really saw what kind of creepy alien was doing that, so it was just an it and that made it extremely alien.
PS: I just noticed that Kanazak and I said pretty much the same thing. And I also noticed that I have no modern aliens. Oh well. I don't even put the x-files aliens into the alien category since if you watch the story really carefully they are not really aliens......anyways.......And yeah, while I have watches movies like Solaris, Contact, and that stupid charlie sheen alien movie with the boy who has backwards legs, I have YET to find a movie made after 1990 that scared me. Why? because they explain everything. Its too perfect, and if we are dealing with aliens they should be UNEXPLAINABLE which is what makes them ALIENS.