"Even though you have been raised as a human being, you are not one of them. They can be a great people, Kal-El, they wish to be. They only lack the light to show the way. For this reason, and above all, their capacity for good, I have sent them you, my only son."
Darker and Edgier: Or perhaps "postmodern?" Even though the movie is a deliberate homage to the Reeve movies, it also brings up the question of his 21st century relevance, makes him a parent out of wedlock and brutally sends him to death's door. Also the colors on his suit are literally darker than in the previous movies.
Data Crystal: The computer in Superman's Fortress. Luthor had some ideas for them.
Dull Surprise: Kate Bosworth was accused of this. Jason can be pretty emotionless at times too.
Eat The Dog: Twice: one of the Pomeranians left in the old widow's mansion ate the other one after Lex left them unattended for an extended period of time, and Lex starts looking at the dog hungrily after he, Kitty, and the dog get trapped on a tiny island.
Enforced Method Acting: In-universe example — Kitty's out-of-control car catches Superman's attention for a damn good reason:
Kitty: I was going to pretend the brakes were out. Pretend! Like we talked about! You didn't actually have to cut them!
Every Helicopter Is A Huey: Superman foils a bank robber attempting to make a rooftop getaway in a Huey, who used the door-mounted minigun to hold off the cops. This doesn't work quite so well on Superman.
Fake Shemp: Unused/recycled footage plus CGI by Rhythm And Hues keeps Marlon Brando in the Jor-El role despite his death in 2004.
Foot Focus: Lois takes off her high heels before her flight with Superman to more easily stand on his boots, resulting in some closeups of her bare feet.
Foreshadowing: When asking Clark about why Superman left without even saying goodbye, he reasons that it was too difficult for him to do so, to which Lois responds in her sarcastic manner; "What's so difficult about saying goodbye?!" At the end of the film, before Superman lifts the Kryptonite continent into space, an act that all involved were almost certain would kill him, he says goodbye to Lois, and it seems she finally realizes what Clark meant earlier.
Go Karting with Bowser: A nasty-looking henchman with a Badger tattoo on his Bald of Evil head passes some time playing "Heart and Soul" on the piano with Lois Lane's son, Jason. Until he tries to kill Lois a short while later.
Held Gaze: Superman and Lois Lane, often. Most conspicuously when he flies her above the city after he returns from Krypton and she's still a bit upset with him for leaving without saying goodbye to her.
Idiot Ball: The only reason for Superman to go off on his own to find out the fate of Krypton. He apparently forgot what he said in Superman II by promising that he'd never leave the people of Earth again, because just one week without him had a trio of supervillains running amuck. So, he leaves Earth for five years. To confirm something his father already told him. Face Palm.
Improbable Age: Lois Lane is played by a 23-year old, and yet already has a kid, a Pulitzer, has worked at the Planet for over five years, and such (by contrast, Margot Kidder was 30 in the first movie).
Made of Iron: Lois. During the plane scene she gets tossed around the crashing plane more than a rag-doll in a tumble dryer, I mean really knocked around the plane's cabin yet walks away from it with nary a bruise or concussion. Sure she passes out but gets up the next day without a scratch.
Magic Brakes: Used as a distraction while Luthor steals some Kyptonite.
Never Trust a Trailer: The first trailer consists entirely of footage of a teenage Clark experimenting with his powers, Martha Kent checking out a mysterious meteor in her back yard, and Lois Lane meeting Superman on a rooftop and looking shocked—all set to Jor-El's narration about why he's sending Kal-El to Earth. This gave a lot of people the impression that the movie was a remake of Superman instead of its latest sequel. The fact that the title hadn't yet been revealed (the posters and trailer just showed the Superman logo on a blue background) didn't help.
Pet the Dog: Oddly enough, Brutus, one of Lex Luthor's henchmen, after watching Jason playing the piano he gently starts to play with him. He turns around and kicks it pretty fast when he catches Lois trying to send a fax, though...
Shooting Superman: To the offending crook's credit, after the minigun rounds failed to do anything, he got the idea that maybe it was the suit that was deflecting the bullets, pulled his pistol out, and then shot Supes in the eye...not only does this fail, but Supes doesn't evenblink.
Shout Out: Many, particularly to the DonnerSuperman. In particular, the airplane rescue scenario is similar to Superman's rescue of Air Force One in the 1978 film, albeit more spectacular in execution.
Spiritual Successor: It's often unclear whether the movie is a sequel to Donner's movie, or an example of this trope.
Stalking Is Love: Superman overhears Lois' address and flies to her house, watching her and her family while hidden outside, using his X-ray vision. He later X-ray-stares at her as she walks out of the office, and flies her above the city for no reason other than to show off and demonstrate that his flying is better than her fiancÚ's.
Storyboarding the Apocalypse: Lex Luthor shows Lois Lane a series of maps detailing exactly how his plan will destroy the Western Hemisphere.
Theme Song Power Up: When Lois' family in trapped in the sinking ship, facing apparent doom with a mournful dirge on the soundtrack. Suddenly, their despair is lifted as Superman arrives to rescue them by lifting the ship to the Superman March.
Took A Shortcut: It is made clear by Jor-El's narration in the first movie that Superman's journey to Earth took thousands of years, but he only aged a few years due to the effects of relativity. Jor-El's comment shows up in this movie when Lex and his goons are in the Fortress of Solitude. Somehow, though, Superman has traveled all the way to the ruined Krypton and back, and only five years have passed by on Earth.
Troll: Lex Luthor has a moment where he acts like this to Lois.
Lex: Come on, let me hear you say it. Just once, come on.
Lois: You're insane.
Lex: No! Not that! The other thing. Come on, I know it's just dangling off the tip of your tounge. Just once, pleeeease.
Wealthy Yacht Owner: First scene in the movie is Lex Luthor swindling an old woman out of her fortune, and among the many things he obtained with it there is a huge yacht-complete with helipad, piano, top-of-the-line electronics, enough room to work on a plan that could destroy the American continent without feeling constricted...