"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."
Chance Meeting Between Antagonists: Lois sneaks onto Lex's yacht (not knowing it's his) and runs into the man himself, while he is brushing his teeth and utterly surprised to see her there.
Character Outlives Actor: Although the character was already deceased in-universe, Marlon Brando's image and old footage was used to portray a dialogue between recordings of Jor-El and Lex Luthor.
Clark Kenting: Given a nod when Lois lists off Superman's measurements and Richard notices that Clark fits the bill, though they quickly brush it off.
Comic Book Time: The film is placed in the same continuity as the first two Christopher Reeve Superman films, yet it is clearly set in the mid-2000s with a 20-something Lois Lane, a still-alive adopted mother, and a still-wet-behind-the-years Jimmy Olsen. The earlier films established that Superman came to earth in 1948 and were clearly set in the late 1970s. This discrepancy is enough to raise doubt as to whether Superman Returns actually is part of the same continuity, but the presence of a photo of Glenn Ford as Pa Kent from the first film serves to establish the link.
Continuity Nod: Many to the DonnerSuperman movies, which are meant to take place before it. For instance, the airplane rescue scenario is similar to Superman's rescue of Air Force One in the first movie, albeit more spectacular in execution.
Contractual Genre Blindness: Evil genius he may be, but Lex Luthor never seems to suspect anything from Kitty's finding Superman attractive or her moral qualms with his nefarious plan, despite already being screwed over under the exact same circumstances in the original Superman.
Conveniently Cellmates: A sequel comic has Lex Luthor pull strings to get a less-than-bright cellmate, specifically so he can have an audience for his genius plans.
Crazy-Prepared: The Daily Planet has prepared headlines for Superman's death or his recovery.
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.
Death by Materialism: Riley, Grant and Stanford would've made it to the helicopter if they hadn't stopped to grab all their stuff, especially all the poker money.
Demoted to Extra: Rising star Kal Penn plays Stanford, one of Luthor's Mooks, and among them gets the lion's share of close-ups, but almost none of his lines whatsoever made it to final cut.
Dull Surprise: Kate Bosworth was accused of this. Jason can be pretty emotionless at times too.
Riley and Grant's reaction to Brutus' death. Especially Grant.
Grant: We had a little problem downstairs. Brutus is dead. He got hit with the piano...
Earth-Shattering Kaboom: In a deleted scene, Kal finds Jor-El's lab relatively intact, however, he flies further and all that remains of the rest of the planet is some debris.
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.
Averted with Lex Luthor's AW109.
Expy: Kitty is basically one to Eve Teschmacher from the 1978 film.
Fake Shemp: Unused/recycled footage plus CGI by Rhythm & Hues keeps Marlon Brando in the Jor-El role despite his death in 2004.
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.
Jason claims that although he has asthma now, his mother (Lois) say's he'll grow up big and strong like his father. Of course, at the time, she thought Richard was his father, but it still applies.
Lex Luthor notices Jason breathing heavily and reacting somewhat fearfully, when he reveals his Kryptonite.
Go Karting with Bowser: Brutus 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.
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.
Jor-El: They can be a great people, Kal-El, if they wish to be. They only lack the light to show the way. For this reason above all, their capacity for good, I have sent them you... my only son.
The film greatly expands upon the allusion in this speech from Superman: The Movie. Besides reusing the God-like floating head version of Jor-El, Superman's return is a "Second Coming", he suffers a "Passion" when Lex and his men beat him up and Lex stabs him in the side, after saving the day he falls to Earth near death in a cruciform position, and he unexpectedly recovers from supposedly fatal injuries, with his empty hospital bed evoking the empty tomb. And as at least one critic (of Time magazine) pointed out, Superman secretly having a child with Lois is sort of like Jesus secretly having a child with Mary Magdalene.
Mythology Gag: When Jimmy Olsen showed Lois and Perry a photograph of Superman, he was so far in the Picture one of them asked if it was a Bird and the other asked if it was a plane.
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.
Another trailer made the movie seem like a basic Superman vs. Luthor adventure with no existential subplot.
Pet the Dog: Oddly enough, Brutus, 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...
Shared Life Meter: The video game has a health bar shared by the entire city, which goes down whenever enemies hurt civilians or cause property damage.
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.
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.
Sweet Dreams Fuel: This seems to be the only Superhero-film ever made that sets out to warm the audience's heart as its primary objective.
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.
Perry White: "Okay listen up. I wanna know it all, everything. Olsen, I wanna see photos of him everywhere. No, I want the photos. Sports, how are they going to get that plane out of the stadium? Travel, where did he go? Was he on vacation? If so, where? Gossip, has he met somebody? Fashion, is that a new suit? Uh, health, has he gained weight? What's he been eating? Business, how is this gonna effect the stock market? Long-term? Short-term? Politics, does he still stand for truth, justice, all that stuff? Lifestyle... Superman returns."
Too Dumb to Live: Lex Luther's cronies. Superman is currently throwing his newly created Kryptonian island into outer space with them still on it, and the entire place is falling apart. Luther urgently tells them to to get the hell out of there and don't stop to take anything so they can make it to his helicopter and escape. So what to they do? Stop to grab as much cash as they can before escaping, which slows them down long enough to be crushed by a pillar.
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.
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...