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. (in Prometheus, it's "Engineer")
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
Could also be subverted by someone watching Rises; "Christ, Nolan!"
Elysium: The production team and Neill calls the Exosuit, the "Hulk Suit" considering that it grants the user immense physical strength. Mind you that it's nowhere Hulk-level, but it works.
Doubles as Genius Bonus: In the production art for the Exosuit, It's spelt "HULC Suit". HULC is short for Human Universal Load Carrier. Its the name of the powered exoskeleton system being produced by Lockheed Martin. In the featurette, The Tech of Elysium, Neill Blokamp describes how the exosuit is based upon technology being developed by the US Military.
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.
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 performance.
Jean-Claude - What some message boards at the time were calling the first movie's water monster.
"The quiver that never runs dry" for Legolas' never-ending stream of arrows.
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
Also "Where Nomad Has Gone Before" due to similarity to the TOS episode "The Changeling".
"Spockalypse Now" has also made the rounds.
Star Trek IV: The Voyage Home - The One With The Whales. Because, as one of the most accessible entries in the series, it's often seen by newbies who forget the title, but remember that there were whales in the movie.
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).
Wreckling/Wrecker: Nickname for a fan of the movie.
Hero's Cuties: The name for the Felix/Calhoun ship, which happens to be canon.
Turbo Twins: The collective name for the two blue-suited racers next to Turbo on the winners' block during the "Going Turbo" explanation/flashback. Fans have come up with all sorts of names for them individually, with Ted & Teddy and Jet & Set being popular ones.