Alien3 tends to be jokingly referred to as Alien Cubed among the fandom due to the inexplicable superscript use of the number 3 in the movie's title.
Space Jockey - the alien pilot aboard the derelict ship — extended to the rest of his race, as well. Derived from a name used by the film crew; in the canon, it's never named.
Xenomorph - Used once, among many other words, to describe the aliens in the franchise, this word stuck as the standard term used by fans.
As a matter of fact, none of the life cycle stages (i.e. Facehugger, Chestburster, Drone) were ever officially named. They were given Fan Nicknames which simply stuck.
Russell - The fandom's name for the scarecrow that Marty crashes into in the first movie.
Wallet Guy- The guy in Part II that tells Biff where Marty went after Marty knocks Biff out. Called 'CPR Guy' in the script (since he asked Marty what CPR is after he mentions it, CPR not having been invented in 1955) but he says he thinks Marty took Biff's wallet at least three times in his scene.
One guy on a Myspace group started referring to Katie Holmes as Katie Who? after Maggie Gyllenhaal was announced as her replacement. After seeing the movie, and the aforementioned plot twist, he changed it to "Should've Been You Bitch". He's a little bitter.
A somewhat more complimentary nickname has been Christ Nolan
LeJoker - Heath Ledger's portrayal of the Joker in The Dark Knight.
Harvey Bullock- Detective Flass, inspired by Bullock, a more prominent member of the GCPD from the comics who somewhat resembles the movie Flass more than the comic Flass does.
Renee Montoya- Anna Ramirez, after a DCAU and Comic character.
Commissioner Atkins- Comissioner Loeb, again, after a comic character who looked and acted more like the movie character than the comic version of Loeb.
Baconface- Twoface, as this incarnation of the villain is extra-crispy.
GINO (Godzilla In Name Only) - The American version from the 1998 film (a later film actually gave it the name of simply "Zilla".). The film itself is often called "Deanzilla".
Ursula Undress - Ursula Andress. If you've ever seen Dr. No, you'll know why.
Most of the films are often referred to by their acronyms, i.e. TLD for The Living Daylights. More amusingly, this is why The World Is Not Enough is sometimes referred to as Twine.
Hock-a-loogie-saurus - Nickname for the Dilophosaurs, also known as spitters, for their ability to spit a loogie of paralyzing poison at its victims.
Chickensaurus - Nickname for dinosaurs of species Gallimimus, since that term roughly translates from scientific latin as "Chicken Imitator".
Munchenaries - Nickname for the Mercenaries hired by William H. Macy and Tea Leoni's characters in the third movie, due to their tendency to be eaten by dinos.
Shityerpantsosaurus - One friend's name for Spinosaurus. He was more of a fan of that movie than most people.
Ong, Ung, Ahng, Oong - Movie!Aang, as opposed to series!Aang. The movie is (supposedly) more faithful to the East Asian roots of character names. Some fans of the series would have preferred faithfulness to the source material over realism in a film where people can shoot fire out of their freaking hands (not that they can do so unassisted in the move anyway, though that's really neither here nor there).
Sowka, Soaka, Eero, Eeroh - Sokka, Iroh, etc. Listen, they're going to be at this for a while. We'll get back to you.
Devko and Peltztara too, because while their characters' names weren't mispronounced, they needed scornful nicknames anyway.
Failbender, The Last Shitbender - The movie itself.
Agent Elrond - Hugo Weaving's portrayal of Elrond the Elf Lord, which was remarkably similar to his Agent Smith portrayal in the Matrix trilogy.
Agent Elrond: You will help us, Mr. Baggins, whether you wish to or not.
Agent Elrond: What good is a ring, Mr. Sauron, if you do not have any fingers?
Agent Elrond: I'd like to share a revelation that I've had during my time here. It came to me when I tried to classify your species. I realized that you're not actually mammals. Every mammal in Middle-Earth instinctively develops a natural equilibrium with the surrounding environment, but you Orcs do not. You move to an area, and you multiply, and multiply, until every natural resource is consumed.
Agent Elrond: Welcome to Rivendell, Mr. Anderson.
Viggo Mortensen said in an interview that in a take of filming the Anduril delivery, Weaving was dressed as Smith, and said: "Mr. Anderson! What are you doing with this sword?".
Figwit - Brett McKenzie's minor, yet absurdlypopular character that shows up in the Council of Elrond. The name itself is an acronym for a memorable fan reaction to recognizing him (Frodo is grea-WHO IS THAT!?). Also called Melpomaen in fanfiction, which is a rough Elvin translation of his name (Melpo = fruit, maen = wit). He only gets a speaking part in Return of the King.
Boromir el Boromido- a play on the words "Boromir" and "dormir" (Spanish for "sleep") and "dormido" ("asleep"). Based on Sean Bean's perceivedly-wooden perfomance.
Jean-Claude - What some message boards at the time were calling the first movie's water monster.
The Burly Brawl - The huge battle between Neo and the army of Agent Smith clones from The Matrix Reloaded. This was its behind-the-scenes name used by the staff, in reference to the screenplay Barton Fink was working on, so it's not technically a FAN Nickname. Indeed, the song playing during that scene is named Burly Brawl on the soundtrack.
Super Burly Brawl - The final batle between Neo and Smith in The Matrix Revolutions.
Not-Bela - The "actor" (actually Ed Wood's chiropractor, Tom Mason) who replaces the late Bela Lugosi after the first few minutes of the film, despite clearly being noticeably taller and thinner than him (and whose only concession to hiding their difference is a cape in front of his face).
The dog with the keys was nicknamed Sammy by fans.
Scruffington - Nickname for Norrington in PotC: Dead Man's Chest
Lt Theodore Groves - most common fanon name given to the unnamed navy officer who says "That's got to be the best pirate I've ever seen" after Jack Sparrow steals the Interceptor. He was identified by this name in On Stranger Tides. His role is expanded in this installment, for he claims the Fountain of Youth in the name of King George II, only to be shot and killed by the Spaniard. "Someone, take note of that man's bravery."
Andrew, most often used fanon first name for Lt Gillette
Bayformers- For the work as a whole and as a description of the unique robot designs. It originally started off as a negative thing, but has progressed to be rather affectionate as a different take on the Transformers mythos.
Agent Megatron - Hugo Weaving's voice work as Megatron in the 2007 movie. Based primarily on his previous roles as Agent Smith and Agent Elrond (see above), as the nickname originated before so much as a leaked sound byte from the film was available.
For the same character and reasons, "Hugotron." And Tankface, because in ROTF his alt-mode is, well...
Itchy- the nameless cellphone Transformer
Americanator- the nameless Pretender from "Revenge of the Fallen" who tries to seduce Sam in the guise of a college student called "Alice". Based on the fact that, according to The Other Wiki, his real form resembles Alice from Alice in Wonderland, thus making it an "evil Alice", like the American McGee one.
Dewbot/Dispensor - the Mountain Dew transformer
Mohawk and Stripe: two of the Transfomers made from kitchen appliances in Revenge of the Fallen. Named after the Gremlins, due to being identical to them (Mohawk was the one from the second movie with fins on its back who drank spider DNA and turned into a spider Gremlin, while Stripe was the one from the first movie with hair on its back who gets killed last).
Doogie Howser, SS - Neil Patrick Harris' disturbingly chilly telepathic Intelligence Officer, whose uniform bore a distinct (and deliberate on the part of the filmmakers) resemblance to those of the Death's-Head S.S.
Also "Doogie Himmler"
Sgt. Revok - Michael Ironside's character, named after his previous role in Scanners
Sgt. Krabz - Clancy Brown's character, named after his later role on SpongeBob SquarePants. Alternately, it is acceptable to call his character Sgt. Hadley
Scottish Lecter, Hannibulldog - Brian Cox in Manhunter, who retains his Scots accent and does a creepy thing with his jaw that makes him look like a bulldog.
The Divorce: The beach scene at the climax of X-Men: First Class wherein Charles Xavier and Erik Lehnsherr's friendship is broken and the sides between Professor X and Magneto officially form.
Dragneto for the deleted scene in which Charles projects an image of Erik in drag to an onlooker. Hilarity Ensues.
Bromance World Tour: term often used for the timeframe in which Charles and Erik traveled around America to recruit mutants. Alternatively called "The Honeymoon".
ceiling!sex: nickname for the rather popularscene◊ in X-Men: First Class wherein Erik pins Charles down on the floor of a spinning aircraft to protect him.
Oliver Splat: Due to the unfortunate fate of Oliver Platt's otherwise unnamed character (who's only listed as Man In Black in the credits)
