These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
There are some fans of the first film that feel the second film did away with the mystery of the original. This in turn has led to fans and critics alike disputing if the first or second film is superior or inferior, with some fans and critics championing the original film by director Ridley Scott as a supposedly more intelligent horror film while degrading the James Cameron sequel as nothing more than a big dumb action movie that just happens to feature alien monsters, while other fans and critics champion Cameron's sequel for fleshing out the lead character while offering a more emotionally complex story and scoff at the original film by Scott for its emotionally flat, vapid characters. And then you have the fans who only like the first two films who just watch this insanity from afar...
On the prequel end of things, Prometheus got hit with this too. It's either a refreshing spin on the franchise that adds more to the universe or a mess plagued with its characters being infected with the Idiot Ball and explains too little about the Space Jockey.
The comic book and novel adaptation which were written between Aliens and Alien 3 are considered the true canon by some fans of the series. Mostly due to the way they expanded upon the characters of Newt and Hicks (with names changed to Billie and Wilks, mind you). They also followed a trend of upping the ante; In Alien, it was more or less a one on one between Ripley and the alien. In Aliens, a war between a team of marines and a swarm of aliens. In the books... Well, that would be telling.
I Am Not Shazam: "Xenomorph" was a placeholder term used briefly in Aliens to describe the aliens. The term means "foreign form" and is not intended to be the name of the species. However, the name has proved easier for fans to use than "the aliens from Alien." Besides, the word itself sounds inherently badass and sinister, very befitting to the species.
In an article in a Traveller RPG magazine - written in 1980 or so, and based on the novelization of the first film - the "Aliens" are described in detail, and called "Reticulan Parasites". In that description, each Reticulan Parasite gives birth to an egg on its own, with no "Mama Alien" present.
The term "Xenomorph" has been used in a few DVD Extras and commentaries to refer to the titular aliens. While it is not their "official" name, it is still considered a semi-canon terminology for them (Much like how Apatosaurus is often called "Brontosaurus").
Iron Woobie: Ellen Ripley. In the first film, she's the sole survivor against a creature which killed her shipmates. In the second film, she gets demoted for destroying her ship in her attempt to destroy the creature, and in the extended cut, we learn her daughter grew up and died during her overextended time in cryo-sleep. When's she's called back by her company to investigate the colony on the planet from the first film, she finds another Iron Woobie in Rebecca "Newt" Jorden, the sole child survivor of the colony's infestation.
Misaimed Marketing: The Alien is one of the creepiest, most disturbing and most sexual monsters ever invented and most of the films of the series contain enough gore and horror to scare kids for life. Yet, it hasn't stopped them from being merchandised, both as toys AND plush aliens and chestburster aliens. The Kenner toyline had such variations as Bull, Mantis, Crab and Jaguar aliens, making it one of the few toylines based distinctly around Bizarre Alien Biology.
Memetic Mutation: The Alien series has a number of famous quotes that are frequently used outside of the film's context. They can be found on the film's YMMV pages.
Narm Charm: There were plans, believe it or not, to make an animated kid's cartoon about Aliens vs Predator. While it never went through, parts of it did make it into a comic book series made for the Kenner action figures, which had Ripley and most of the marines from the second film surviving Acheron, and subsequently going on GI-Joe style missions to battle Aliens throughout the galaxy, wearing brightly colored uniforms, sprouting endless one-liners note "HUG THIS!" and wielding goofy, cartoonish weapons (Ripley wields up a flamethrower that's bigger than she is). When compared to the dark and gritty terror of the film, the whole series is hilarious (read it here).
Also notable is a predator who appears to be wearing nipple cannons
Nightmare Fuel: Ever-present in the series, even in the works that focus more on action than suspense.
Sequelitis: Notably avoided by Aliens, a great sequel which is widely considered to be as good as the first film. The third and fourth installments, and especially the AvP films, however, are considered a major step down. This is largely explained by the reasoning why the films were made. James Cameron was a fan of the original Alien and wrote the script to Aliens on spec. He was told that if The Terminator was successful he'd be allowed to direct the sequel he wanted to create, making it a labor of love. By Alien 3, however, the producers (who had meddled with the script of the first film) were making a sequel for the sake of the franchise. As such they burned through a bunch of different scripts and ended up with an amalgam of different attempts. Things didn't get any better from there. A number of people view that Resurrection might have been a pretty good film (a beloved screenwriter and a notable director with a solid grasp of visual style and atmosphere) if it hadn't been shoehorned into the Alien universe.
Viewer Gender Confusion: The Aliens themselves, especially the Queen who is often called a "she" in the films. Technically, all members of the species are hermaphrodites (i.e. having both male and female sex organs) from a visual viewpoint, because H.R. Giger's design is neither male nor female but a disturbing combination of both sexes. From a reproductive viewpoint, the series tends to flip-flop between the Aliens being actual hermaphrodites (Giger's own original portrayal of the creature included human-like sexual organs, a scene deleted from the first movie had the alien being able to "convert" two humans into huge eggs with fully-grown aliens developing inside, the original design for the Newborn From Resurrection was that it was, like Giger's original model, possessed of a human-like vagina and penis) and the Aliens being asexual "drones" where selected individuals can mutate into/be hatched as parthenogenetically fertile female "queens".
Applicability: Ridley Scott said that there is no allegory, freudian, feminist, marxist, or otherwise to be found in this film. That has done nothing to stop decades of endless analysis of this film's use of H.R. Giger's excessively freudian imagery and the role of Ripley as a feminist icon, among other things.
Alternative Character Interpretation: Ash: he's a strong android with medical knowledge, he could have killed Ripley in three seconds if he really wanted to. Instead, when he moves against her, he starts flipping his shit and acting all deranged. Many viewers take this as indication that he's suffering from a programming conflict: he's supposed to help humans but his orders are to sacrifice the crew if necessary. His later comment on the alien being free from "delusions of morality" takes on a new light, then: he wishes he didn't have any sort of morality chip at all. And his distaste for humans can seem understandable when you consider that he is a slave, like other androids in the Alien universe. Why should he be expected to care for them? He isn't given much of a choice, either, and is just as much a victim of the Company as the other characters.
The other idea is that he actually is malevolent, beyond that which he is programmed for. The idea being that, in part, he is fascinated by the alien and wants to emulate it (That being the reason behind his method of killing Ripley), and actually has motives of his own, beyond simply studying the beast, indicating a degree of A Iis A Crapshoot.
Ensemble Darkhorse: Jones the cat. In the actual movie he barely has any screen time and when he does, all he does is hide, hiss and run away. However the trailers and later TV Spots make it look like he's just as important as the Alien and Ripley.
Freud Was Right: The aliens, full stop. Also the Derelict ship, not to mention some scenes. It's H. R. Giger, what are you expecting?
Dan O'Bannon: This is a movie of alien interspecies rape, that's it, that's scary, that scaring because it hits all of our buttons, all of our unresolved feelings about sexuality, all of them.
There is a lot of rape symbolism, such as Ash rolling up a porn magazine and forcing it down her throat, and Lambert's death, complete with offscreen noises that sound like violent orgasms.
And on top of that, the chestburster scene is all about a phallic creature bursting out of a man's stomach like a horrific self-induced C-section.
Idiot Plot: Dallas made a few boneheaded decisions. Most notably bringing Kane and the facehugger back on the Nostromo without following the 24-hour quarantine rule, even though Ripley is telling him it's a bad idea and it means breaking the law. Granted, he did it with the best of intentions (trying to save one of his crew) and he remains a fairly likeable character.
Seinfeld Is Unfunny: When the film was released in 1979, there were reports of viewers running into the theater lobby to throw up. This seems strange in retrospect, because the scenes of Kane getting chestbursted and Ash getting his head knocked off are positively tame compared to the later Slasher Movie and Torture Porn genres, or the Body Horror achieved by Carpenter's The Thing (1982) or Cronenberg's The Fly.
The Woobie: Lambert, especially if you add in the deleted scenes. While she somewhat comes across as a whining bitch, she has a few establishing moments in the deleted scenes that paint her as a notably more sympathetic (if not necessary more likeable) character, which makes her tragic demise even more gut-wrenching.