In Alvin and the Chipmunks Meet the Wolfman, Alvin believes that the neighbor Mr. Talbot is a werewolf, but Dave and Simon (the latter playing along regardless) brush him off though Simon very readily justifies this with a record he kept of everyone that Alvin thought was a werewolf, mummy, vampire, or she-wolf, which had practically everyone in town. But for once, it turns out that Alvin was right all along, considering that Talbot is the werewolf that bit poor Theodore and turned him into a were-munk.
In Cars 2, Sarge gets the idea that Miles Axlerod may be lying about the safety of Alinol, so he swaps it out with Filmore's organic fuel, which ends up saving McQueen's life.
Sarge: Once big oil, always big oil.
In How to Train Your Dragon 2, Stoick is completely right in claiming that Drago Bludvist is beyond reason and that he will turn his dragon army on Berk.
In Recess: School's Out, TJ Dettwiler tries to tell everyone in town that there was suspicious activity going on at the school, yet his parents and the police never believed him, and his friends felt doubtful at what happened after stealing one of their crates and Prickly apparently leaving the school (It Makes Sense in Context). Turns out, TJ was actually very sound in his suspicions, as the school had actually been taken over by an extremist group led by the former Secretary of Education and former principal of Third Street Elementary, Phllium Benedict, that was trying to eliminate summer vacation.
Disney's Robin Hood has this with Trigger the vulture, one of the Sheriff's lackeys. When a blind beggar comes up to the gallows where he and the Sheriff are, and he and the other vulture, Nutsy, start carelessly saying that they're going to hang Friar Tuck at dawn. Only Trigger is suspicious of him which is justified, since the beggar is Robin in disguise. Early the next morning, an hour before dawn, Trigger continues ranting to the Sheriff about how he knows that there's going to be a jailbreak. The sheriff dismisses it as paranoia, even as Robin Hood and Little John infiltrate the grounds. He gets his vindication the hard way an hour later, when he tries to warn the Sheriff again, and it turns out to be Little John in disguise.
Rear Window (and its newer equivalent, Disturbia): guy stuck in house becomes increasingly convinced his neighbour is a murderer. Guess what?
In the HBO movie Safe House, Patrick Stewart plays an old man who is suffering from the early stages of Alzheimer's disease. He tells his caretaker that he used to be a DIA agent and people are out to get him because He Knows Too Much, so he insists on elaborate security precautions bordering on the ridiculous. Until the end, it's unclear whether his paranoia is justified or if he's just a crazy old man. As it turns out, they really are out to get him.
The Mel Gibson movie Conspiracy Theory features an obsessive-compulsive paranoid conspiracy theorist... who turns out to be mostly right, though he's more remembering than speculating.
The Thing (1982), by John Carpenter, features a shape-shifting alien capable of infecting and duplicating every living thing. The characters are right about not trusting each other, and try to come up with a way of figuring out who is the thing and who isn't, but generally are unable to do so until Nightmare Fuel time sets in.
Though played straight for most of the film, it's horrifically subverted in the case of Clark. He seems to be the most likely candidate for being infected as he was alone with the initial Thing for quite some time, and doesn't have an alibi for most of the cases of sabotage that one or more infected has been behind. In the end, it's later proven that he wasn't one of the infected... after MacReady has already shot him through the skull. Childs makes sure to point out that MacReady screwed up royally in that respect. (Although, in fairness to MacReady, Clark did try to attack him.)
Freeze Frame, a British film, where the main character films everything he does, 24/7/52, after been accused (but acquitted) of multiple murders. It finally allows him to prove himself innocent in the end. It stars Lee Evans (a comedian) in a serious role.
In GoodFellas, Henry is called paranoid by his wife and associates for having suspicions about a helicopter follow him all day long, as well as being extremely scared that his mob friends are going to whack him any moment. Unfortunately, he was correct to be paranoid, as the helicopter belonged to the DEA finally intending to arrest him, and Jimmy really wanted to whack him because he was going crazy as well.
Chance warns the others about being sent to the pound every chance he gets in Homeward Bound: The Incredible Journey. Sure enough when they encounter the people searching for the lost girl, Chance is wary of them for this reason. Three guesses where the people drop them off, and the first two don't count.
In Bowfinger, a movie star prone to paranoia is driven to even wilder hysteria when a small film crew shoots a dramatic movie starring him without his knowledge. His Scientology-like counselors fruitlessly try to calm him down until they discover the film crew and note "Well, I guess it's true; it's not paranoia when someone's really after you."
In Ferris Bueller's Day Off, Cameron doesn't want to leave his dad's prized Ferrari at a garage in the care of a sleazy-looking attendant. He does so only after some persuasion by Ferris. It turns out his worries were absolutely justified as the attendant and his friend take the car on a joyride only seconds after they leave, adding dozens of miles onto the car.
The President's Analyst, soon after taking the title job, worries for his own mental health when he thinks he's seeing Men In Black following him everywhere, and has a nightmare that his girlfriend is a spy. Turns out he's right on both counts.
Horrible Bosses: Harken's paranoia throughout the film that his wife Rhonda might be cheating on him is portrayed very unreasonably and dumbfounded. In the end, however, this is proven correct when Rhonda gives Kurt a blowjob in the bathroom during Harken's surprise birthday party.
Strange Days reveals that the extreme misfortunes and frequent assassination attempts following the main characters around stems from a death squad operating within the LAPD designed to target undesirables, including a prominent rapper-slash-social activist who was recently assassinated. When one character dismisses this as paranoia, a Properly Paranoid one rebuts that "it's not a question of whether you're paranoid, it's whether you're paranoid enough." The other characters spend the rest of the movie in a state of deep paranoia about this. Except it's a complete lie; the rapper was shot by two trigger-happy cops who merely screwed up a traffic stop, most of the other events of the movie are the result of various other plans and gambits crashing into each other chaotically, and the Properly Paranoid character was in on it the whole time and made up the whole 'death squad' thing on the spot to distract from his own wrongdoings.
In The Phantom Menace, the Jedi council is reluctant to take Anakin Skywalker on as an apprentice. They probably should have followed that instinct. On the other hand, it was also, in a way, their shutting him out that caused him to turn to the dark side.
Star Wars Palpatine was always fearful of his apprentices turning on him . Hence why he does things like grooming young Jedi and Sith to be future apprentices in case his current one got out of hand. And purposelessly placing his strongest apprentice Darth Vader into an outdated limiting life support suit despite having the tech and budget to give him a much more current life support suit. Later Vader offers to overthrow him with Luke's help so the pair can rule the galaxy together, so the Emperor was not really wrong.
Marvin in the film adaption of RED believes he was being used in some secret government mind control project. It turned out that he actually was being fed LSD for decades. And that's just the beginning of the list. Literally EVERYTHING that Marvin becomes paranoid about is either true or becomes true over the course of the film.
Bob Lee Swagger in Shooter. Religiously, obsessively protective of his guns, which turns out to be what clears his name when he is framed for an assassination. Taking the firing pins out of his rifles when he puts them away would be just as effective at preventing accidents or unauthorized use, but Bob goes the extra mile and replaces them with custom-modified pins that will not fire. The only reason for this would be to fool someone who was deliberately trying to frame him, and who would know to check the firing pin. Which means he planned for that exact scenario. Bob has good reason for his paranoia; he's been back-stabbed before.
In the Halloween series, others viewed a young Michael Myers as a disturbed boy. Loomis viewed him as a monster just waiting to strike. Guess who was right.
In Galaxy Quest, when the crew of the NSEA Protector goes on a planet to search for beryllium spheres to repair the ship, one of the crew members, Guy, panics when he sees the planet's residents. Naturally, the crew dismisses this as paranoia because he once played a Red Shirt on the show who died in an episode before the first commercial. In a hilarious turn of events, Guy is proven right.
Guy: Sure, they're cute now, but in a second they're gonna get mean, and they're gonna get ugly somehow, and there's gonna be a million more of them.
Guy:Did you guys ever watch the show?
Sarah Connor from the Terminator films. She even gets institutionalized for this, but it turns out there really are killer robots from the future after her.
In Transformers: Dark of the Moon movie, Jerry Wang is convinced that everything is a Decepticon. He is later killed by his computer, which then turns into the copy machine, and poses variously as a TV, stereo, and pink Bumblebee.
Tremors: Though not a straight example, having an underground shelter with Wall of Weapons and ammo, supplies and a power generator in case of World War III served Burt Gummer well when his town got attacked by large subterranean carnivore reptiles.
Earl: Guess we don't get to make fun of Burt's lifestyle anymore.
I, Robot: Del Spooner (played by Will Smith) doesn't trust robots, believing that they are not as safe as the Three Laws of Robotics are supposed to make them. He is therefore the only person in Chicago who doesn't get one of the new NS-5 model robots. When the NS-5s stage a Zeroth Law Rebellion, Spooner is naturally the only human capable of effectively fighting back. It was his Properly Paranoid and bigoted attitude that allowed Dr. Lanning to pull a Batman Gambit on him to save the day, kicked off by Dr. Lannings own death.
In The Dark Knight, Harvey Dent doesn't try anyone of Gordon's unit which is made of many corrupt cops. Two of those cops would help Joker to kidnap Dent and Rachel.
Played with in The Departed. Mob boss Frank Costello and the police captain that is investigating him both assume that the other has planted a mole in their organization. They're both right. However, both miss out on catching the moles, and neither realize that each side has more than one mole at work.
Yello Dyno of Tricky People apparently has a habit of patrolling the mall and accosting anyone he even suspects of being a "tricky person". The one time we see him doing this in action, he turns out to be right.
The Tom Hanks black comedy The 'Burbs is all about this trope. Hanks' character is convinced by his friends that the creepy neighbors on their block are actually serial killers. They repeatedly try to find ways to expose them, but all they succeed in doing is to continue making fools of themselves. Then at the end the suspected neighbors confront Hanks, and it turns out his friends were 100% right.
In 28 Days Later, after an attack by the Infected leaves Mark with an open wound and covered in blood, despite his protests that it's his blood, Selena says she can't take the risk and immediately hacks him to death with a machete. Since it takes only a single drop of blood to become infected and the person will turn in 30 seconds, Selena has a very good reason to be so paranoid.
Naomi Harris has said that she believes the reason for this is because Selena had to kill her entire family after they got infected...including her younger brothers and sisters.
Marty, the resident stoner of The Cabin in the Woods, is convinced that something strange is going on and that there are puppeteers running everything. His friends ignore him. At first. Later, when one of his friends admits that he was right, he says he wasn't. What he'd uncovered was much bigger.
In Saving Private Ryan, Reiben is against letting their prisoner "Steamboat Willie" walk free, in case he's picked up by the Germans and "thrown back into circulation." Which is not only what happens, but the ex-prisoner also fatally wounds Miller.
The protagonist in Take Shelter sees himself as this when he begins digging up his backyard to expand their storm shelter. Everyone else thinks he's gone nuts.
Basil from The World's End. He's a conspiracy nut who drinks from a crazy straw so "they" can't get his DNA. "Not so crazy now", when it turns out his entire town is infested with blanks.
In The Hobbit, Bard is the Only Sane Man who recognizes that Smaug could and would bring destruction to Lake Town, reminding them what had happened to Dale, but he is ignored out of common greed. Smaug flies off to destroy Lake Town at the end of the second film. Later on, he tries to place the last Black Arrow on the large crossbow in case Smaug does come, but is stopped by the Master.
Patriot Games: Professor Jack Ryan is leaving work when he notices a young man that looks like Sean Miller idling nearby. The man casually walks away as he notices Ryan looking at him, but Ryan is clearly unnerved, even more so when he hears a car engine starting up. And with good reason—as he continues to walk down the street, the audience sees that both the car and the man are now following him. Luckily, Ryan quickly notices this too and is able to disarm the man—the woman driving the getaway car is unfortunately able to escape—and foil the attempt on his life—revenge for Ryan having foiled an assassination attempt made by these people several months earlier. The interesting subversion is that Ryan had been warned about the possibility of this by his CIA contacts—it's he who didn't want to believe that the group would go to such lengths to kill him.
A Series of Unfortunate Events: Every single one of Aunt Josephine's fears and phobias previously waved off as ridiculous by the children (including the stove bursting into flames, the fridge crushing one flat, and the door-knob exploding and a fragment getting in one's eye) come true after she disappears. Every. Single. One.
Violet:[as the door-knob is superheated, and about to shatter]No way.
In Godzilla (2014), Joe Brody's obsession with his wife's death has left him more than a little nutty, but he was still right about the cover up.
X-Men: Senator Kelly is concerned about mutants that can enter the mind of others or walk through walls. As it turns out, Mystique has been impersonating his aide for a good long while.
X-Men: First Class: On multiple occasions, Erik warns Charles that humans will turn against mutants. At the end of the movie, he is proven right, as the United States and the Soviet Union unite forces to launch an attack on the group of mutants who has just saved their lives and prevented World War III.
X-Men: Apocalypse: Upon learning that someone who might be Magneto is in their midst, the Polish police who come to arrest him intentionally leave their badges and guns behind, using only bows and arrows in order to prevent him from using metal against them. Unfortunately, they were not quite paranoid enough, as he instead uses the locket with his parents' photos in it that Nina has to kill them all.
Gavin from Disturbing Behavior, a seemingly drug-addled teen is convinced there is some kind of mind control conspiracy going on in Cradle Bay but is rebuked by Steve when he claims he is next. Not only is he 100% right, but they also get him.
In Enchanted, Robert is rightly suspicious of the fact that people keep trying to give Giselle free stuff. These "people" are actually Nathaniel, who tries to slip Giselle poison apple in some form or another from the moment he's first able to get to her in New York.
In Primer, second act, none of what we see is actually the first timeline. This means there are time travelers from alternate futures running around doing who-knows-what.
Aaron: What's worse? Thinking you're being paranoid or knowing you should be?
In The Conversation, Harry Caul does everything in his power to keep his privacy intact, to the point that he keeps his office phone unlisted (and he makes calls through public phones if he needs to contact someone) and it's a serious, relationship-shattering Berserk Button if anybody asks him too many questions about anything (especially personal info). Then it turns out that the company that hired him to record the titular conversation made a very thorough dossier on him even before he was hired and there is absolutely nothing that they don't know about him and there is absolutely no place that he owns that they can't break into to steal from him or place a bug.
Yello Dyno from Tricky People apparently has a habit of patrolling the mall and accosting anyone he even suspects of being a tricky person. The one time we see him doing this in action, he turns out to be right.
In Even Lambs Have Teeth, Katie calls her Uncle Jason "a crazy, paranoid cop" for insisting that she call him every day, or text him if she can't call. He also makes her put a code word at the end of each text and change the word every day in case someone else gets hold of her phone. However, when she is kidnapped by sex traffickers, they use her phone to send him a text saying everything is fine, but they fail to change the code word. Jason is immediately suspicious and goes to investigate.