Star Trek Into Darkness was particularly dark, even after the previous film's destruction of Vulcan, with a villain whose attacks on Starfleet recalled al-Qaeda terrorism and the revelation of a semi-fascist xenophobic warmongering faction within Starfleet.
As with their book counterparts, the Harry Potter films became increasingly dark and serious starting with Prisoner of Azkaban, but this is evidenced most in the last three sequels, both in terms of cinematography and subject matter. The first two films were full of warm golds and reds, while the later films favour cold blues and Deathly Hallows is almost black and white. To further hammer this fact in, "Hedwig's Theme", which introduces each film, sounds slightly shriller and more discordant in each consecutive film. But after Voldemort was defeated in the last film, the vivid colours of the first movies return.
At some points in the final three films the action, which is easy to see when watching in a dark cinema or room, is hard to see in a bright room with sunlight shining in.
Revenge of the Sith. This sequel manages to be the darkest of all prequels, and probably the darkest of the entire saga so far. (Notably, it is the first and so far only Star Wars film to garner a PG-13 rating). This is where you know the plot of the Fallen Hero, The Bad Guy Wins this time and this is the first in the series that blood shown graphically (note when Anakin is almost killed).
An in-universe example in the obscure flick Adventures In Dinosaur City, where a trio of kids find themselves zapped into the world of their favorite cartoon. Where things aren't just good guys and bad guys like they are on the show, and the story's about as gritty as they could get away with in a kid's film while not losing the aesop about there being no such thing as Black and White Morality.
Batman Returns becomes so dark it becomes a Stealth Parody since Burton couldn't really replicate the feel of the original Batman books and his characterization of Batman almost completely removes his most notable trait: Thou Shall Not Kill.
Babe 2: Pig in the City is very much this trope compared to the original. The original was about a little pig on a farm who was taken in by the female sheepdog and was mostly lighthearted. Tear Jerker here and there, but the darkest element was when Babe's parents are herded to the slaughterhouse. In Babe 2, there's a hotel with illegal pets, animal control, a vicious bulldog that nearly hangs him trying to kill Babe, and one of those little wheelchair dogs who almost dies. Terrifying for some kids. On the other hand, in the first part a duck is killed for the Christmas dinner and a sheep is killed by feral dogs and in the second part no animal is Killed Off for Real.
Richard Kelly wrote a screenplay for Louis Sachar's lighthearted Black Comedy, Holes, that went in this direction. Instead of searching for buried treasure at a juvenile delinquent summer camp, the movie would have had the boys searching for nuclear weapons in a post-apocalyptic Texas. One scene has Stanley visiting a prostitute. The studio instead used the screenplay written by Sachar himself.
A common trend in films about King Arthur, which is a pretty downbeat legend to begin with.
Excalibur combines Magical Realism with gritty, bloody violence, reaching a peak of dark edginess in an early scene in which a knight in blood-stained armour tricks the wife of his nemesis into having sex with him. There are plenty of impalings and crow-pecked corpses to go around as well.
Robert Bresson's Lancelot du Lac. What it lacks in gore and Dung Ages ambiance, it makes up for by being extremely dour, mechanical and joyless, Bresson films are wont to be.
The "historical" film King Arthur from 2004 has the Knights of the Round Table turn out to be just a pack of Roman mercenaries fighting evil Saxons in a cold, windswept wasteland of an England.
Licence to Kill is by far the darkest of the series to that point. It starts with Colombian drug lord Franz Sanchez feeding Bond's longtime friend and ally to a shark (after raping and killing his new bride), followed by Bond resigning from MI6, going rogue, and killing every member of Sanchez's organization in increasingly graphic ways.
The Daniel Craig Bond films, starting with Casino Royale are darker and more realistic than previous Bond films, going deeper into Bond's pathos and doing away with most of the wisecracks, gadgets and slapstick. Skyfall also goes in for Deconstructor Fleet, Dented Iron, serious questions about everyone's sanity, and The Bad Guy Wins by killing M although his victory is indirect as he is killed by Bond before M kicks the bucket.
The second Home Alone film is much less lighthearted than the first, taking place in New York rather than a Chicago suburb, and with Kevin using much more dangerous traps against the Bandits. Also, when they catch him, Harry fully intends to murder Kevin. Ultimately, it ends up arguably being an Even Better Sequel.
The third film takes it even further...but is generally considered a flop.
TRON: Legacy is much more grim than the 1982 original. When you got programs violently shattering into data, genocide, a brutal dictator, and brainwashing programs to invade the real world, you got more than just the suits and the environment that's darker than the first Tron.
The Black Hole itself qualifies on its own. Released in 1979 it was controversial for being Disney's first PG-rated film, and featured numerous violent and disturbing sequences the likes of which no Disney film had ever shown before. Even the resident "funny robots" were not actually that funny and were played straight. Although it took a few years, the move towards more adult fare exhibited by Black Hole, Tron, a rather adult comedy called Trenchcoat and others eventually led Disney to establish the Touchstone brand for releasing films in the PG, PG-13 and R-rated realm, while reserving the main Disney brand for (mostly) G or the occasional PG film. This later went by the wayside however, as the Disney brand came to be used for dark, PG-13 rated films like Pirates of the Caribbean.
Speaking of Pirates of the Caribbean, the sequels fall into this. The second film pits Jack against a threat he can't talk his way out of and, in the process, puts more emphasis on his morally ambiguous side, with him resorting to genuinely shady stuff to escape his Deal with the Devil. The third opens with Cutler Beckett presiding over a mass execution - and becoming the first Disney villain to kill a child onscreen. Elizabeth and Will both have to join in the speed chess game just to keep up, with Elizabeth getting the big Shoot the Dog moment of leaving Jack to face the Kraken so the others can escape. And the fourth film, with no Will or Elizabeth, has no characters involved in the main plot who aren't utterly self-serving, and falls into Affably EvilVersus Not-So-Affably Evil.
G.I. Joe: The Rise of Cobra had EVERYONE wearing black and a knives and bullets always finding their way into enemy eye sockets. Then we have the Baroness display her cleavage and the buxom Scarlett wearing a sports bra while on a treadmill. Not to mention a guy's face is literally DISSOLVED by his own nanites!
The sequel, G.I. Joe: Retaliation, was darker and less cartoonish than the original, even featuring the death of Duke, the hero of the first movie.
The the original animated TV series, despite being about a paramilitary group assigned to combat a terrorist organization, was nonetheless intended to be child-friendly, i.e. A-Team Firing galore, and despite the fact Scarlett was armed with a crossbow, she'd never consider using it to actually, you know, kill anyone. Perhaps reflecting the post-9/11 attitudes that A Team Firing is unrealistic and cheesy, the GI Joes of the live action film (and recent-vintage animated reprises and the comic books) are depicted as you'd expect a paramilitary force fighting terrorists would be - ruthless killers each with double- and triple-digit body counts. Even Scarlett.
The original G.I. Joe: The Movie is way darker than the animated show. Its revealed Cobra are led by an ancient race of reptilian beings, most of the familiar cast are held prisoner by giant alien plants for the entire film, we follow a new team of rookies as they struggle to replace the Joes, Cobra Commander devolves into a giant snake with 100 eyes, Roadblock goes blind, Duke DIES (and is revived thanks to Executive Meddling adding unconvincing ADR).
The Transformers series in general. Robots are getting ripped apart, blown up, or their faces bifurcated. The added sex (and not much else) is supplied by Megan Fox.
Although amputation, decapitation and on at least one occasion, crucifixion, were all features of the 80s transformers comics.
And the third film cranks it Up to Eleven, with humans being assassinated, as well as having Sentinel Prime launch a full scale Decepticon assault on Earth, complete with scenes of carnage.
Ghostbusters II might not be as good as the first movie, but it sure is darker than the first, involving an ancient god in a painting looking to be reborn in a baby, people's emotions manipulating and being manipulated by pink slime under the city, and our heroes (temporarily) being put in an insane asylum at the beginning of the Darkest Hour.
Back To The Future Part II compared to the first movie. Why? 3 reasons. 1, the alternate 1985. 2, in the alternate timeline, Biff marries Lorraine after killing George. And 3, Doc Brown is institutionalized in the alternate timeline.
Snow White & the Huntsman compared to almost any other adaptation without a doubt. From the trailers alone, we can already see that this movie is way more violent, with epic-scale battles and soldiers smashing each other to pieces left, right and center, has very scary-looking creatures, and throws in a few nasty twists such as the Queen really being a much older woman that sucks the life out of much younger women to preserve her youth. Oh, and if that weren't enough, almost the entire film and its settings are very dull and colourless, whereas in most other versions, the kingdom and most parts of the forest are much more colourful and presented as nice places to live. Here? Not so much.
The movie also has a much more serious tone than the first movie. Movie Superheroes Wear Black seems to be in effect, with Cap wearing a darker, more practical outfit rather than his colorful costume from The Avengers, and The Falcon wearing dark military gear rather than his red costume from the comics. Scarlett Johansson specifically said large portions of the film invoke the Not Wearing Tights trope to give the movie a more "grounded", realistic feel.
Free Willy 2 & 3. Compared to the first movie, in which the only tearjerker was Willy almost dying. The second had Jessie nearly drowning and getting incinerated by an oil tanker fire. While the dangers there were unintentional, the third amps it up by having human villains not capture the whales, but try to kill them and sell their meat to underground markets. Willy's not exempt from this either since in the climax of the film, he actually almost kills the captain of the whaling ship for attacking him, his mate and their unborn child.
Alien³ is a much darker film compared to the one that preceded it. In fact is like riding a train to downer land. Aliens was a fairly standard action film with an overall happy ending (and that isn't a bad thing). Its sequel however has an air of hopelessness that just pervades the entire thing. Two major characters are killed right at the start and another one is damaged beyond repair, the film is set on a grimy prison planet populated by murderers and scum, there is almost nothing to fight the alien off with so more characters, even likeable ones, die left and right (often with no build-up), and even Ripley is killed off at the end because it's the only way she could stop The Company from bringing the Alien gestating inside her back with them. Sure things get better with "Resurrection", but that doesn't exactly raise spirits either (due to quality rather than tone)
The events and the characterisation of the family members in the The Addams Family films are significantly darker than they were in the TV series, although still not as dark as some of the original Charles Addams single-panel cartoons.
The Wolverine is more serious than the previous X-Men movies, presenting the story as a noir crime drama.
X-Men: Days of Future Past adapts one of the darkest X-Men storylines ever, and, while it has many humorous moments, the overall tone (especially that of the Bad Future scenes) is pretty bleak.
The Future Sentinels, more than their typical adaptational portrayals, especially the in-story 1970's versions.
''Look Who's Talking, Too! focuses on James and Mollie's marriage possibly faltering and Mikey & Julie's Sibling Rivalry. It climaxes with James fighting an armed robber and their apartment burning down.
According to The Tracking Board, the film adaptation for Sonic the Hedgehog is supposedly getting this treatment, though because a script has not yet been written, it's too early to tell.
Saving Private Ryan compared to a lot of other earlier war movies. Established very quickly with the opening Omaha Beach battle - you're introduced to The Squadonly for nearly all of them to be slaughtered extremely quickly, and a lot of the poor sods who bite the dust do so in extremely graphic ways (the flamethrower guy who goes up and takes out a few surrounding soldiers, the man who's in a state of shock and walking around looking for his severed arm, the young soldier lying on the ground trying to hold his intestines in, the radio guy who winds up with no face, etc). Not to mention it's one of the few American war films you'll ever see that depicts American soldiers committing war crimes.