Bleach: Kubo quite likes dropping little hints that only become important later (in fact he's announced that EVERYTHING becomes important at some point in the Final Arc), so this is only a partial list.
In the beginning of the manga, one of Ichigo's first Hollow-hunting assignments dealt with Orihime and her hollowfied older brother. Ichigo reveals his belief that a big brother is born first to protect the younger siblings that follow. This becomes significant during Ichigo's climactic battle with Byakuya where he berates Byakuya for failing to protect his younger sister Rukia.
During the Soul Society arc, Rukia, Byakuya and Ukitake were all struck by the physical and psychological resemblance Ichigo bears to the late Kaien Shiba. A couple hundred chapters later, it's revealed that Isshin, Ichigo's father, was originally a member of the Shiba clan. Ichigo and Kaien look alike because they are first cousins.
In fact, Byakuya's comment about Ichigo resembling Kaien also foreshadows something else. He tells Rukia at the beginning of the Soul Society arc he understands her desire to protect someone who looks so like a man she misses keenly. It's only at the end of the Soul Society arc that the readers learn that Byakuya's late wife Hisana was the spitting image of her younger sister, Rukia, that he made a solemn deathbed promise to Hisana to protect Rukia, and that he was forced to disregard that promise until her false conviction was resolved.
Yumichika's true shikai is hinted at in the Soul Society arc when he fights Hisagi, but it takes about 200 chapters to actually see it in action.
Uryuu's brief use of Letzt Stil against Mayuri, when he starts absorbing reishi so rapidly that he destroys surrounding buildings. It's the first mention of "reishi enslavement" as a Quincy capability. Fast forward 400 chapters, and the evil Vandenreich has a modified form of Letzt Stil called Vollstandig capable of the same feats but without the one-time-only drawback...
In the Soul Society arc when Choujirou is ordered to attack Ichigo, he states the name of his zanpakutou, Goryoumaru. An old-fashioned reading of the kanji for "goryou" is "lightning". Hundreds of chapters later, it's eventually revealed that his Bankai gave him the power to control the weather to produce lightning as a weapon. During the Zanpakutou Arc anime filler, the anime team asked Kubo to design the zanpakutou spirits, so Goryoumaru is actually seen using lightning-based powers, also foreshadowing the eventual reveal.
At the end of the Soul Society Arc, Ukitake quietly gave Ichigo a badge meant to mark him as a sanctioned substitute Shinigami. And yet, Uryuu thought something was off about the situation and the Mook guarding Kurakara Town didn't recognise it. The Chekhov's Gun took about 5 years to fire: The badge is a spy device and Ichigo is only the second person one to receive one, after Ginjo Kugo. Ichigo reveals even he suspected the thing was a fake after a couple weeks' reflection.
Shinji's introduction to Ichigo's classroom where he mentions backward writing as a particular talent. His first appearance in the storyline (his first appearance in the manga was actually on the Chapter 1 cover) walking upside down in the sky drinking water as if he was right side up. More than 200 chapters later, we learn his zanpakuto's ability allows him to flip the perception of its target so all directions are reversed.
Ichigo's hollow kept on calling himself the "real" Zangetsu, as if the Zangetsu Ichigo was using was somehow false. It was a manifestation of Ichigo's Quincy power and the Hollow was a manifestation of Ichigo's real Shinigami power.
The revelation that Ichigo's Zanpakutou has been a false one all along explains why he is the only Shinigami using a compression Bankai. Unlike Shinigami, Quincies draw in power from around them to use in battle. Ichigo's Quincy power manifesting as a Zanpakutou meant his "compression Bankai" was influenced by these Quincy rules.
When Uryuu was first properly introduced, there was a a title page◊ where Ichigo (the Shinigami) was right side up and Uryuu (the Quincy) was upside down, symbolizing their mirror-image relationship. This recurs on the title page of Chapter 189, wherein both boys are struggling with choices about their powers and their values. This takes on a whole new meaning when we learn that the Vandenreich's shadow dimension actually exists underneath Seireitei.
Dragon Ball Z pretty much foreshadows Goku's first transformation to Super Saiyan all throughout Namek.
There are many, many examples in Dragon Ball. Including:
From Goku's first transformation into an Oozaru and him turning to normal after his tail is removed, Oolong asks if "he's some kind of space alien". Turns out he's a member of the Saiyan race.
In the beginning of Z, Raditz when he arrives on Earth makes reference to the Galactic Market which he's a mercenary for. The good guys then have to face off against the head of the organization, Freeza.
The first time the "Super Saiyan" is mentioned, it's between a conversation between then-introduced characters, Vegeta and Nappa as they head off to Earth for the Dragon Balls to grant them immortality. It's mentioned again once more sarcastically by Vegeta describing Gohan's resilience in the same saga, and in the Namek saga, the Great Elder asks Krillin if a Super Saiyan was the one killed Kami, before learning his actual nature. The term is used far more frequently as a plot-point after Vegeta suspects Goku became one after curb-stomping Recoome, by Vegeta, Ginyu and Freeza, until Goku finally achieves it facing Freeza.
Piccolo becoming less evil, and allowing the people he killed (Raditz) to pass on. While it shows he is changing into a Noble Demon, it also ominously notes that his life may end soon.
King Kai noting that if Vegeta was at Krillin's mercy and was killed, it wouldn't "[destroy] the roots [of evil]". He was likely referring to Freeza.
Nail noting Piccolo as a one of two beings (Kami), and remarked if they united again, he'd be more powerful than Freeza. He did this later and was strong enough to go toe-to-toe with Imperfect Cell.
Freeza tells Zarbon that he may need to call the Ginyu Force to Namek. When Zarbon ask why, Freeza mentions that he had a "premonition" that a single Saiyan may come to challenge his power, and even has the possibility of defeating him. Interestingly, he wasn't talking about Vegeta. It's likely it foreshadowed Goku (or alternatively, Future Trunks).
Ignoring Future Trunks' message, looking back on it, it can even be implied that Bulma and Vegeta may get together, when she offered him a place to stay alongside the Nameks in her home, although at first sight it would be simply her being a decent person as an Earthling would be. She even described a dream she to her then-boyfriend Yamcha about Vegeta being a decent guy to her. Of course, this is just a few episodes just before Trunks appears.
Kami being reluctant to fuse with Piccolo to observe if the artificial humans are really as evil as Trunks claimed they were, and observing a new evil developing (Cell). Turns out he was correct. Not only were they not as evil, Cell was and then some.
Goku noting that Majin Buu is more of a Man Child than an evil monster, after their fight. He is redeemed after the Enemy Without was destroyed by Goku, and decides to spare his life.
Also with regards to Buu there is a possibility in one of Fat Buu's comments to Babidi. While dancing around in mockery of Babidi's injuries, he chants "Never normal, never normal, can't go back, can't go back!" In later episodes, Buu goes back to "normal".
Full Metal Alchemist
Madame Christmas of Fullmetal Alchemist seems like a strange name when you remember that Christmas or Christianity are not in the manga version of FMA. Of course it makes perfect sense when it's just a nickname based off her real name of Chris Mustang, who is Roy's foster mother. That explains how he became such an amazing flirt.
Fullmetal Alchemist does this quite often, usually with things said in passing by the homonculi. "Human Sacrifices" indeed...
In episode 11 of Brotherhood, a wanted poster with Greed on it appears near the end. Guess who appears two episodes later.
There's a particularly chilling example in the most recent arc. In Chapter 94, Hawkeye gets a minor scratch on her neck during a fight with Envy. Then in Chapter 100 she is mortally injured in the same place.
Remember Lust's curse to Mustang as he killed her? I long for the day your eyes are twisted in agony. Well... Mustang ends up blinded.
In his fight with Lan Fan, Ed uses a decoy (in the form of his detached right arm) to defeat her and references getting the idea from animals who are trapped sacrificing a limb. Later on, Lan Fan is hunted by Wrath and forced to chop off her arm.
In fact, it is heavily implied that Lan Fan actually took the idea from Ed's trick.
Ling and Greed are the only two characters to go around without shirts. Minor foreshadowing? Maybe.
A better example of foreshadowing for Ling's fate occurs soon after his introduction: Ling is seeking immortality and is interested in Al's soul being attached to armor. Guess who else shared these same traits and was killed off in the chapter right before.
There's also the part where both of them hate people fucking with their henchmen. Really, they were tailor made for one another.
When Ling sees Ed perform alchemy without a circle, it looks to him as though Ed is praying to God. Later, we find out that Amestrian alchemy is powered by a Satan-like Homunculus who actually absorbs God, only to eventually lose control at the apex of his power and receives a No-Holds-Barred Beatdown sans alchemy courtesy of, umů
The first anime had major foreshadowing for the manga. . Example 1: Mustang's defeat of Pride in the final episode has a lot in common with his defeat of Lust in the manga (both homunculi impale him with their respective weapons during the battle, and both are ultimately killed by Mustang burning them with his bare hands until their regenerative abilities are exhausted. Example 2: At the end of the anime, Mustang loses an eye. Guess what? In the manga he goes completely BLIND. Example 3: Riza Hawkeye emotionally shoots Archer to death after thinking Roy is dead. She does the same in the manga to Lust but it doesn't work in the latter case. Heck, even tiny things as Ed's Conqueror of Shamballa hairstyle looking eerily similar to his hairstyle in the manga's final arc and the stealth crowd appearance by Ling foreshadow the manga's events in various ways.
Greed's first words. Really...
Greed: Ooh, cool! He really is empty!... Nice to meet ya, kid. I'm Greed. Wanna be friends?
Go watch any, or all, of the openings to FMA Brotherhood. One would notice that they all have a close up of either Roy's face and eyes. In some he looks directly at us.That coudn't mean anything right?
The initial filler episode of FMA Brotherhood has Isaac Mc Dougal asks the Elric brothers, "Do you know what shape this country is in?" In episode 35, Ed realizes that this was meant literally. Amestris is in the shape of a transmutation circle With the points of the circle quite literally marked in blood.
Mahou Sensei Negima
Say, remember how in the early chapters of Mahou Sensei Negima!, there was that Negi is a prince rumor that spread in Negi's class? Guess what's been revealed more than two hundred chapters later?
Not to mention this statue, which also appears in that chapter, is quite closely related to Negi's royal lineage. The mage just so happens to be Negi's direct ancestor, and the first Queen of Ostia.
There's more. When Asakura first witnesses Negi's magic, she briefly wonders if he might be on a (genderflipped) version of a Magical Girl Queenliness Test, or that he may be a hero of justice or an alien. Negi was actually sent to Mahora as some sort of test, and as the above spoiler shows, he's technically a royalty, so the Magical Girl Queenliness Test thing was partially correct. And then there's Negi's quest to become a hero like his father, fitting the hero of justice one. Lastly, his mother was born on Mars, so he's also technically an alien.
Even earlier, there was this, which is the first time Negi's father is shown. The foreshadowing part is what appears to be the shadow on the right side of his face, which shows up again here, and eventually revealed to be blood (spoilers). It's subtle, but that hint of blood is the earliest hint of the Genre Shift that the series would eventually undergo.
The same page shows Nekane on the ground behind Negi, which becomes more significant in Volume 8 when we find out that she was petrified and her legs were shattered in Wilhelm's attack.
Chapter 29 has a scene where Negi and Chao have the exact same expression and mannerisms when listening to Yue's explanation. In chapter 82, Chao claims that Negi is her ancestor.
When Yue and Nodoka ask Negi if they could become mages, there's an imagine spot showing what they think it will look like. Some 140 chapters later, it turns out that their imaginations were spoton.
And that image spot continues to foreshadow "more than two hundred chapters later" (seems to be a theme for Negima) as it may look a bit different, but we finally get to see Nodoka confident and wielding a magical staff.
Back in the "School Festival" Arc, Negi questions Chao about why she has an insane technique that drains the body and soul for unbelievable power. Cue the next major story arc where he learns an insane technique that drains body and soul for unbelievable power.
From the cover of Volume 3◊, look at the logo on Negi's shirt. It's the Ala Alba symbol.
Chapters 164 and 165 seem like just a humorous interlude, and perhaps the silliest moment is when Makie goes into the confessional only to complain that she can't think of any worries to get off her chest. 133 chapters later, Makie is one of the only ones unaffected by a Lotus-Eater Machine, because she's so satisfied with her current life that the real world is her ideal world. Unexpectedly, Chisame is also unaffected, and suffers a Heroic BSOD at the thought of being just like Makie in that aspect.
Ku Fei makes a joke about the number of Fate existed back in the day and shudders to think that there may be more. In Chapter 311, guess how many showed up.
At one point, Negi, Nodoka and Yue head into Library Island looking for Nagi. They are stopped in their search by a dragon, who ends up drooling on Nodoka and Yue, prompting Yue to state will will one day get her revenge on the dragon. Different dragon, but many chapters later, Yue proves her worth during her Laser-Guided Amnesia by her role in taking down a dragon.
One of the earliest ones was smack in the beginning of the first chapter. The small space between Negi and Asuna clearly shows Zazie with long, sharp claws. More than two hundred chapters later we learn she is actually a demon.
A minor one in Naruto. In chapter 91, Gaara casually mentions Shukaku is more blood thirsty during the full moon. Over 350 chapters later, it is revealed the body of the creature the Shukaku was born from is sealed in the moon.
A really realllyyy long-in-the-coming revelation: when Itachi confronts Sasuke after the Uchiha Massacre he tells him to read the tablet below the Naka Shrine in the Uchiha household. Sasuke does as told, but his eyes are always blackened out when he does so. Some 300 chapters later we find out that the tablet was created by the Sage of The Six Paths himself and can only be read (partially) by the Sharingan and more fully by the Mangekyou Sharingan and Rinnegan. The foreshadowing? Sasuke actually unlocked his Sharingan for the first time during the aforementioned confrontation with Itachi, but he also saw Itachi cry shortly after that and could not cope or understand that, and so he repressed the memory along with his knowledge of activating the Sharingan.
During Kakashi's bell test early in the series, Kakashi places a kunai on Sasuke's neck and tells Sakura, "Kill Naruto or else Sasuke is going to die". Hundreds of chapters later the same scenario is played out again in the back story of a major villain (except that this time it was for real).
Itachi's parting words to Sasuke: "When you have the same eyes as I, come to me." Originally he was talking about Sasuke acquiring the Mangekyou Sharingan eye power, but now Sasuke has Itachi's eyes transplanted on him and he runs into a resurrected Itachi.
More words from Itachi, but this time to Naruto: "If now that you are powerful you start to forget about others, to be arrogant and to be attached to your ego... One day you will become just like Tobi." Which implies that Tobi was just like Naruto in his early days before turning evil. Which is later confirmed to be true, once it's revealed that Tobi is actually Obito Uchiha.
Another one regarding Tobi's identity: At one point Kakashi attempts to use Kamui against Tobi, only for him dismissing it by saying "Don't bother, Kakashi, that technique doesn't work on me." Several chapters later we learn that the technique Kamui and Tobi's powers are connected, because Tobi is Obito Uchiha from whom Kakashi's Sharingan comes from.
Ever since Rock Lee and Guy introduced the eight inner gates and the lethal consequences of opening all of them people have been waiting to see it happen to one of them. Guy opened the last one in order to fight Madara, and his father Might Dai died from using Gate of Death against the original Seven Ninja Swordsmen of the Mist.
While Princess Kaguya being the real Big Bad was somewhat of an Ass Pull, there was some foreshadowing that she was more sinister than we thought. For one, her violent tactics caused her to be feared as a demoness than hailed like a goddess like she was initially. Then an offhand comment reveals that she had used Eternal Tsukuyomi once before. However, the most prevalent piece foreshadowing comes when Madara activates the genjutsu once again; her silhouette appears to overlook the landscape with a very visible and very startling Slasher Smile on her face. That was the most visible clue in that despite her good intentions, there was something off about her.
After it's third transformation, Juubi senses chakra of Bijuu & Sage of Six Paths within Naruto, causing it to freak out. After that it charges a massive bijuudama in order to finish Naruto off. However, it does something unusual for a bijuu, forming a hand seal. This unexplained rage from an entity which was supposed to be devoid of any feeling as well as doing something a human does to control chakra was indication about it being more than just what characters told about it till that point, which now fits with revealation about Kaguya's history.
The Rain Ninja in the Chuunin Exams seemed unduly interested in Naruto and Gaara. Turns out, the Akatsuki are based out of the Rain Village, and they are after Jinchuriki.
One Piece is the king of this trope. Author Oda often drops thing that foreshadow events years and/or hundreds of chapters in advance.
Luffy stating that even though it is shortening his lifespan, he wants to use 2nd Gear to protect 'what is in front of him now'. It's a noble sentiment, but it wound up foreshadowing the Wham Episode when he uses it, but still fails to protect his True Companions from getting poofed by Kuma.
Usopp's lies often turn out to be foreshadowing as well.
During the Alabasta arc, Sanji makes frequent references to and jokes about 'okama' (Japanese equivalent of 'drag queen') while fighting the cross-dressing Mr. 2, Bon Clay. Later, he ends up on an island of gay men. Who all really, really like him.
The Amazon Lily arc seems to be a payoff to earlier foreshadowing. Between them, Boa Sandersonia and Boa Marigold use via Ambition (or Haki, if you prefer) abilities remarkably similar to Skypeia's Mantra, CP9's Life Return, Garp's ability to physically harm Luffy despite his rubber body, suggesting all of these are forms of Ambition which the previously seen users may or may not have known about.
In the Jaya arc, Buggy the Clown's crew contemplate taking an ideal chance to kill Portgas D. Ace when he falls asleep on their ship. Buggy warns them against it because the one thing Ace's captain Whitebeard will not tolerate is the death of his crew. The Impel Down and Marineford arcs center on the Marines preparing to publicly execute Ace, even though it will certainly mean war with Whitebeard.
In 2006, there was an anime special, where the Straw Hats were mythical animals. Luffy was a dragon. Guess who turned out to be his father? The revolutionary Dragon, the world's most wanted man.
Related to that revelation, way, way back in Chapter 5, Zoro asks Luffy if he's the offspring of the devil. Four hundred and twenty-seven(!) chapters later, we find out that Luffy is the son of Dragon, who the World Government considers to be the "The Worst Criminal in the World."
When Nami first joined the crew in the Buggy Arc, she said that she'd only join for the time being, and that she would eventually leave the crew, was obsessed with money, and showed a suspicious hatred toward pirates. She actually did leave the crew at the end of the Baratie Arc to confront Arlong, an abominable pirate who had made her life miserable and struck a deal to buy Cocoyasi Village from him for 100,000,000 berries- a deal which he later screwed her over on.
That pirate in Shank's and Buggy's flashback in the first few chapters from when they were cabin boys? It turns out that he's Silvers Rayleigh, the former first mate of Gold Roger.
Oda reportedly insisted that he not be named captain when the flashback was animated, only revealing the reason why almost a decade after the fact.
In the Impel Down Arc, Blackbeard alludes that he's soon going to "make a show that will shake the world to it's core", he means this both literally and figuratively as he somehow steals (something that is noted to be usually impossible) the Gura Gura no Mi at Marineford.
Back in Loguetown when Luffy was about to be executed by Buggy, a lightning bolt strikes the platform, frying Buggy and leaving Luffy miraculously unscathed. In the Skypiea arc, we find out that Luffy, as a rubber man, has immunity towards lightning and specifically towards Enel's powers.
At the end of the Enies Lobby arc, Kokoro mentions to get to Fishman Island the Straw Hats will have to pass through a sketch of sea that is haunted where there were reports of haunted ships. Luffy immediately asks if they will get to see skeletons that move. Which does come true when the crew meets future crewmate Brook, a living skeleton.
Even before then, Luffy has been adamant for getting a musician as a crewmate and repeats this desire several times. It comes true when Brook joins.
Earlier on, Nami is shown to have an exceptional weather sense and when comes her Alabasta fight, the weapon that she asked Usopp to make for her has to do with weather control.
In the first chapter of One Piece, Shanks scares away a sea monster with just a glare and later on, he knocked out several crew members of Whitebeard's crew. In Skypiea, Satori and Aisa were also shown to have an ability to sense other people's presence and even predict their moves. When fighting Duval, Luffy manages to stop Duval's bull, much to his and everyone else's confusion. This ability would be revealed to Haki, which wasn't expanded upon until Luffy arrived on Amazon Lily and later trained with Silvers Rayleigh.
A triple case of foreshadowing:
When Don Krieg first appears at the Baratie, he and all of his men have just escaped the Grand Line, after losing 49 ships in their fleet, with only the flagship surviving the mass sinking. Even so, the crew, captain included, is nearing starvation, and the flagship has been shredded up by cuts and slashes, like someone attacked it. Turns out Don Kreig's crew crossed paths with Dracule "Hawkeye" Mihawk, the greatest swordsman in the world, and he decimated them.
But that's not all: Hawkeye followed them all the way back and returns to finish the job, sinking the flagship. And on top of this, Zoro begins to freak out when he learns who is in his sights, because he promised Kuina he would become the world's greatest swordsman and continued to work towards this dream after she died in her honor. Zoro immediately challenges him to a duel to the death, despite the difference in their skill level. Hawkeye mows down Zoro in battle, breaks two of his swords, and inflicts an enormous scar on his chest, because Zoro claims that the scars on a swordsman's back are his worst shame. Hawkeye admires his honorable qualities and makes his finishing blow-non lethal so they will meet again. They end up meeting again, and Zoro asks Hawkeye to be his mentor.
And considering the matter of not having scars on one's back, Whitebeard is ravaged by all manner of injuries to his front side until he dies, but not one single scar is earned on his back- he NEVER ran away.
When Ace first appears, he is chasing after the pirate Blackbeared for murdering a fellow shipmate on Whitebeard's crew and abandoning them like scum. Blackbeard is also said to have attacked the Drum Kingdom, sending Wapol and his forces running because of their dirty cowardice. Some time later, Luffy runs into Blackbeard at Mock Town, who seems unusually jovial and goofy to be the aforementioned monster... until Luffy learns that he's the reason Ace was sent to his death.
When Luffy's reunion with his brother Ace finally ends in Alabasta, and he leaves, he says he'll meet Luffy again "at the summit" (meaning when he's a top-level pirate, he'll see him again). When Luffy next sees Ace, it takes place at the "Paramount War" in Marineford with the Whitebeard Pirates and their allies fighting the Marines and the Shichibukai to save Ace's life.
Shanks meets up with Whitebeard to warn him of the potential threat of "Blackbeard" Marshall D. Teach and asks him to call Portgas D. Ace back, saying he isn't ready to face him. Whitebeard's refusal not only leads into the greatest war the world had experienced in recent history but led to his and Ace's deaths, and Teach even taking over his old territories and "Yonkou" status.
Laboon. The whale that the Straw Hats encounter in their arrival at the Grand Line - it was restlessly beating itself on the cliffs and calling for someone... That someone turns out to be Brook, who was stuck in an analogue to Bermuda Triangle for many years and who subsequently joined the crew, to fulfil his promise of going around the world and coming back to meet Laboon at the starting point.
The cover of Chapter 668◊ shows us the gravesite of Ace and Whitebeard. In front of Ace's grave is a box with a bottle of sake and 3 cups on it. Who placed those there? Seems minor at first, until you realize that later on, Chapter 731 all but confirms that Sabo is alive and he was the one that placed the bottle and cups at the gravesite as a tribute to his friend Ace. He, Luffy, and Ace drank sake together once before as kids as a sign of brotherhood.
The opening narration to Haruhi Suzumiya foreshadows a lot of the upcoming plot, and one fact that is so spoilery that it can't even be mentioned on this page.
Additionally, both Yuki and Mikuru give Kyon cryptic warnings that, after the fact, seem incredibly obvious.
In the first (chronological...chronological discounting Time Travel) episode, we get some foreshadowing for the second season. Impressive considering they weren't sure there would be a second season at the time.
Haruhi: Have I met you somewhere before? Like, maybe in the past? Kyon: Not that I know of.
A few months into Kyon's subjective future, he time travels to the past, where he helps Loli Haruhi draw a giant symbol on the school quad at night. She didn't get a good look at him, but obviously this hasn't happened for him yet.
Also in the same episode:
Taniguchi: She drew this weird giant symbol on the school quad! Snuck in at night to do it! Kunikida: Oh yeah, I heard about that. It looked like one of those Nazca drawings. Kyon: And she did all this herself? Taniguchi: No doubt!
Same as the above—Kyon was the one who drew the symbol, under Haruhi's directions. She didn't actually help at all.
Yuki is reading Hyperion when Kyon first walks in. A major plot point of the first two books in that series is a computer intelligence that has started creating Artificial Humans one of which is murderously violent and another that is very helpful and honest and in the second half of the Hyperion Cantos God (okay, Jesus) turns out to be a Genki Girl that drags a helpless boy along on her adventures that potentially threaten the entire world.
Koizumi makes a few off-hand references to the student council before they become a plot point. In Live Alive, he mentions that he heard about Haruhi's "big activity" from them, and during Day of Sagittarius, when Kyon assumes the student council has finally come to shut down the club, Koizumi mutters "You're right, that hasn't happened yet..." We eventually find out he engineered the election of a new student council president, one who would be able to act like the enemy Haruhi was expecting.
Naraku gives Sango a choice: steal Inuyasha's Infinity+1 Sword for him or he'll kill her brother. He then tries to kill her with it, something he shouldn't be able do since it's protected by an anti-youkai barrier. Later, we find out that Naraku isn't a youkai. He's a hanyou, just like Inuyasha: hanyou aren't repelled by the barrier which is why Inuyasha can use it.
As a result of the same scene, Sango warns Inuyasha's group that if Naraku ever gives her the same choice again, she'll make the same decision again (betray friends to try and save the life of a loved one). In the Final Battle, Naraku gives her the same choice (kill Rin to save Miroku's life) and, true to her earlier warning, she does indeed make the same choice again (fortunately, Kagome saves Rin's life just in time).
Another throwaway comment, this time by Toutousai. When Inuyasha first masters the Kaze no Kizu while fighting Sesshoumaru and it's revealed at the same time that Tenseiga has chosen Sesshoumaru as its true master, Toutousai mutters to himself "Whether Tenseiga lives or dies will depend on Sesshoumaru's heart". It takes hindsight to show us just how significant that statement proved to be.
Early in the manga, the concept of daiyoukai is introduced when it's revealed that the killer of Inuyasha's father was Ryuukossei. Inuyasha's father stabbed Ryuukossei through the heart, but it only sealed him, not killed him. When Bokusenou tries to explain Inuyasha's Super-Powered Evil Side to Sesshoumaru, he struggles because Sesshoumaru's so powerful he's never been cornered into a desperately life-threatening situation. Towards the end of the manga, Sesshoumaru is finally put into the desperate situation when Magatsuhi, the most powerful youkai evil in history, thrashes him and stabs him through the heart. It neither kills nor seals him, instead unlocking his true power. Sesshoumaru promptly surpasses both Magatsuhi and his own father, achieving Daiyoukai status in the process.
He's actually watching a fictionalization of the Second Impact, and the characters are lamenting science's inability to detect the deadly meteor before it struck. The irony being that there was no meteor to detect, Second Impact was a man-made event.
Let's not forget Ritsuko's lamenting on the Hedgehogs Dilemma. Some fans connect this with Shinji's choice regarding Instrumentality.
In Episode 7, the head of a rival robotics manufacturer mockingly compares the EVAs to "A hysterical woman". Then, much later, we find out that the EVAs each contain the soul of their respective pilot's deceased mother...
In the opening sequence, we see many images of characters and plot important words. After showing a picture of Kaworu and Rei, the word 'Angels' appears.
Not to mention a shot of Yui Ikari in profile, followed immediately by a shot of a helmetless EVA-01 in profile. The credits, like the rest of the show, like to mess with your head.
A bit of musical foreshadowing occurs during fight scenes. Note one of the Angel themes is titled "The Beast"; compare with whenever EVA-01 goes berserk, the theme is titled "The Beast II", referencing how Evangelions are living beings.
Although only noticeable in the english translation the Mechas are all called EVA which can be read as Eve who is infamous among the Abrahamic Religions. This hints to the fact that they're all actually the Pilot's Mother in Giant Robot Form.
Episodes 15 and 16 set the tone for the last half of the series; Dark secrets start to come to light, character relations start to show instability (well, more than they already were), and otherwise takes a step back from the more upbeat atmosphere of the earlier episodes. Most telling of all is the violent return of a Berserk 01 at the end of ep. 16. It all sets the stage for the series' first major Gut Punch, and the more infamous aspects of the show.
Happening very early in the anime adaptation of Seirei no Moribito, some kids are singing "The Nahji Song/Song of the Nahji", which represents events that happened in the past, and those to come.
Misuzu's fate in AIR gets foreshadowed a lot by Yukito's remarks. The viewer then gets fed false hope when things seem to be alright after the "last dream", but it all ends pretty much as predicted.
Princess Mononoke: After San is temporarily incapacitated during a fight, Lady Eboshi warns her men that she's still dangerous with the words, "If you cut off a wolf's head, it can still bite." Now try to guess what rips Eboshi's arm clean off late in the movie.
Also, while fighting Ashitaka, Eboshi declares, "Why don't I just cut the damn thing off?" in regards to his cursed arm.
In episode eight of Digimon Adventure, the group stays at an abandoned mansion. While there, TK notices a picture of an angel, and explains to Patamon that it's a benevolent guardian, comparing it to the digimon themselves. At the end of that story arc, Patamon digivolves into Angemon and gives his life to protect TK.
You'd surely never see it coming: at the beginning of Read or Die the OAV, Yomiko wakes up and hums Beethoven's "Ode to Joy"; later on, it's revealed that the true threat is Clone Beethoven and his Suicide Symphony.
Also, when Joker first fills Yomiko in on the robbery of the DNA of famous people, a list of the individuals whose DNA was stolen is shown behind him. The name on the bottom of the list? Mata Hari.
Gundam SEED does this with incredible subtlety. It's pretty much seen in the first ending sequence, which is essentially a wide shot of all the important characters, namely the crew of the Archangel, the 4 ZAFT pilots, and Lacus Clyne. However, there is ONE important character missing. Mwu La Flaga. Lt. Raimus happens to be staring at a soldier's helmet and a dog tag on a cross. The kicker? The ruins of the Strike Gundam in the background. And that's THE FIRST ENDING! This was planned quite well.
Rau Le Creuset is missing too.
In the manga Mobile Suit Gundam Wing: Battlefield of Pacifists, Heero teased that Duo came along with him on a mission, because he got into a fight with Hilde. Fastfoward to the Frozen Teardrop novel, Duo and Hilde are divorced.
5 Centimeters per Second : You know the tune of the background music in the scene where Takaki and Akari part ways when they're 13 after meeting for the first time in years? Sure is pretty, ain't it? It's actually taken from a pop song, which supposedly pretty much everyone in Japan has heard about. It's about a man who persistently longs for his doomed love. If you know what the song is about beforehand, then you probably had a pretty good idea of where the plot of the movie was going.
There's quite a few moments of foreshadowing in the original Chrono Crusade manga that made it into the anime, only to never have the payoff work out thanks to the Gecko Ending. This includes Chrono's Unstoppable Rage tendencies becoming a major plot point, to Rosette's watch causing her to appear as a ghost to people in the Order later being a key to raising her from the dead.
In the Sailor Moon manga, Chibi-Usa creates a clay replica of the Holy Grail two chapters before the real thing is introduced. The clay Grail subplot also exists in The Ninetiesanime, but the search for the Holy Grail is made the entire focal plot point of that arc in the anime, so it loses some of its foreshadowing properties. Ironically, Chibi-Usa's decision to give her clay Grail to Hotaru in the manga foreshadows Sailor Moon's decision to give the real grail to Hotaru in the anime.
Kannazuki no Miko has lots of foreshadowing, such as quick, very short flash-backs of the priestess ritual seen a few times. The whole first part of Episode 8 heavily hints that Chikane's ''up to something'', and watching the show several times will induce cringing during some seemingly perfectly innocent moments, such as Chikane commenting that she likes the color of Himeko's robes better than her own or even just Nekoko saying she doesn't like to get injections... There's also the fact that on the painting-thing of the Orochi, seen in the very first episode, the eighth head is quite obviously separated from the others and won't be seen at first glance.
At one point in the Spiral manga, Hiyono starts spouting out Kanone's "data" ; he stops her when she's about to say his father's name. Said name is revealed about three books later, said father is central to the plot. ... And the reason Hiyono knows that name is more than the fact she's got insane info-collecting skills. As all Hiyono manages to say is "Ya" before Kanone angrily interrupts her, though, it seems like some random pained cry the first time you read it. (And that's how it got "translated" in the English publication.)
Oburi is hit by a basketball thrown by a little girl near the beginning of Kite, in the process splashing water on the back of his coat. At the end of the series, he walks past the same little girl as she innocently bounces a basketball off of the wall... right before she nonchalantly pulls out a gun and shoots him in almost exactly the same spot.
There's about a million examples in Revolutionary Girl Utena, but one in particular happens during the "Freaky Friday" Flip episode. Utena makes an off-hand remark about how she feels like she's gotten caught up in a bizarre ritual, and that she hopes she can get out before someone is sacrificed. Since it's on this page, it turns out that's exactly what Akio has been using Anthy for, and he's trying to build Utena up to replace her.
When Haruko first hits Naota with her guitar in FLCL, she yells "lunch time!" and in the final episode what does she do to Naota? She yells lunch time and feeds him to the terminal core. Doubles as a Call Back.
Yu-Gi-Oh! GX: Daitoukuji makes mention of Juudai's true power sleeping in season one. Then, Kagemaru insists that he must duel Juudai to gain his power over Duel Spirits and attain eternal youth. It's not just Juudai's power to communicate with them (Manjoume is there as well, after all) but as we find out later, Juudai is the incarnate force that created the universe itself!
Tengen Toppa Gurren Lagann has a bit pretty early, and about halfway through: The first major time is when Kamina says "Simon, without you, I'll die." Guess what happens in episode 7 and 8 where they have separate objectives (Kamina and the rest of the Gurren-dan were to distract the enemy, so Simon could use Lagann to take over the Dai-Gunzan). The second time is in episode 15, when Simon has just killed the Spiral King, Lordgenome. Lordgenome then warns Simon about what will happen when the population reaches a million. Guess what happens in episode 17 (albeit 7 years had passed between episode 15 and 17, so people had forgotten the warning).
A subtle one occurs in the second episode. After having just broken out onto the surface, and faced with another Gunman, Simon starts to run away from it, not wanting to fight a machine bigger than theirs. Kamina, having just made another defiant speech, just watches Simon as they flee and calmly asks, "When are you going to stop running, Simon?" This is followed up in Episode 7, during the team's first fight against General Thymilph. It's Simon who figures out how to win the battle, and Kamina pointedly crosses his arms, giving his little bro full control over Gurren Lagaan. (When the enemy curses Kamina's name for their defeat, he nonchalantly replies "Hey, that wasn't me.") One of the pivotal points of the series is Simon becoming The Determinator after Kamina's death, carrying the Dai-Gurren to the end of the series.
Death Note takes this to the next level. In the first episode, Ryuk tells Light "When you die, I'll be the one writing your name in a Death Note". In the last episode, Light survives several gunshots, only to be killed by Ryuk writing his name in the Death Note.
In the Shaman King anime, in the first episodes Manta tells Yoh he's seen a boy like him, meaning he saw someone who's a Shaman like him. Yoh then says that he doesn't have a twin, joking. Turns out he does have a twinbrother, as we find out several episodes later. Not sure if this is foreshadowing though, since his words were more like an accidental guess.
Absolutely everywhere in Puella Magi Madoka Magica. Why are characters (especially Kyouko) often depicted eating something? What does cooking eggs have to do with the worth of a woman? When you rewatch the episodes after you watch episode 10, you're going to cringe at the Foreshadowing.
During the girls' first (shown) conversation at Mami's apartment there's an interesting shot where the reflection of Mami's head on the glass table is shown superimposed over her legs, as if it were lying in her lap. Come episode 3.... Later in that same conversation there's another shot where Mami's entire torso is bisected by the glass, letting us know *exactly* how Charlotte eats her meals...
In the very first episode, Madoka mentions having a dream about Homura before actually meeting her to Sayaka and Hitomi. Sayaka jokes about the two's fates being intertwined, having must met each other across time and space, and how Moe Homura is. This takes on a new meaning in Episode 10, where it's revealed that Homura has gone through a "Groundhog Day" Loop to protect Madoka, and was originally a bespectacledShrinking Violet with Girlish Pigtails.
In the films of the anime, when Sayaka becomes a magical girl and saves Madoka a snippet of Symposium Magarum is slipped into the otherwise spritely music of the scene.
In Tiger & Bunny, there's a curious tendency throughout the series for Barnaby's Troubled Backstory Flashbacks to be a bit inconsistent with each other — such as the same event taking place in different settings, or a person's clothing/appearance changing ever-so-slightly from one flashback to the next. This is one of the first hints that someone's been messing around with his memory.
On a playing card◊ for Tsukiyo, Luna the doll is already standing and holding onto the sofa without any assistance. And on this page, the telescope smacks Keima's head but Tsukiyo and Keima's hands aren't anywhere near it.
Two from Digimon Savers. When Touma is formally introduced to Masaru's mother and little sister, he's briefly saddened, but develops a sort of crush on them almost at first sight, and approaches spending a day out with them the way some men might plan a marriage proposal. While the episode includes a brief flashback to his own mother, confirming he has issues with her, it's a good twenty episodes before we find out that he also has an Ill Girl little sister that he dotes on. A subtler one is from episode 8: When he reveals that he planted a listening device on Yoshino, assuming that she'd ignore orders to back down from a target she was too close to, Touma adds that "To deceive your enemies, you first have to deceive your friends." Halfway through the series, Touma pretends to betray the group in order to get close to and betray Kurata, who's holding his sister hostage.
In The Grand Punk Railroad, Isaac and Miria have a conversation about the name of Frankenstein's monster, with Isaac insisting that the monster's name was actually Mary Wolstonecraft Godwin Shelly. When Miria points out that Mary is a girl's name and that the monster was male, Isaac counters that men sometimes have feminine names and there's no telling what sort of name a monster would have. As it turns out, the entire conversation is a nod to the true identity of the Rail Tracer (a monster slowly offing people inside the train), who is revealed to be a male assassin named Claire.
In Eyeshield21, Sena's test number for the Deimon test entrance exam was 21.
Way back in the earlier chapters, Agon predicts that Ojou would make it to the top 4 at best. Ojou got 3rd in the Kanto tournament, and 4th overall.
A random member of the Dinosaurs suggested "they should just aim for 3rd", which is what Hakushuu ended up getting.
During the game against Shinryuuji, Monta catches a ball thrown by a fan without even turning around, foreshadowing his later move "the Devilbat Backfire" which wouldn't officially appear until the game against Ojou.
Pandora Hearts may as well be called Foreshadowing: The Manga. Examples include but are not limited to: Oz's strange and sudden attachment to Alice after having just met her (he was her stuffed rabbit doll one hundred years ago), Raven's gold eyes and black hair (he's actually Gil ten years in the future), the state of decay undergone by the coming-of-age ceremony mansion (ten years passed while Oz was trapped in the abyss), Gil's hardiness and fast recovery rate (he's a Baskerville), Cheshire's single red eye is actually Break's missing one, Break's weak constitution and his tendency to cough up blood (Mad Hatter is only his second chain, the first having resulted from an illegal contract), Jack's assertion that he's not a hero (he's the villain), Alice's sense of foreboding on recovering certain memories (they were the memories of when she killed herself to protect Oz), and even Oz's name (he was named after Oswald-Glen by Alice one hundred years ago). And that's not even including the enormous amount of foreshadowing and symbolism that's prevalent in Jun's artwork (a site analyzing it can be found here).
K dropped a few subtle hints throughout its episodes:
The opening song showed Yashiro falling from the sky. It's significant, as he was thrown off the Silver King's blimp before the series started but has no recollection of how and why.
Shiro lacks a cell phone, one thing that tells perhaps most about the owner - friends, acquaintances, personal information. It's because his memories are all fake and implanted by Neko.
Shiro is highly competent, such as knowing how to pilot a helicopter, deducing information like a scientist would, and knowing exactly how to work flash bombs. It turns out that he is actually Adolf K. Weismann, a German war scientist during World War II...
In episode 1:
Kukuri said that she keeps an eye on Yashiro because it feels like he would disappear if she didn't. Later, she had no idea who he is, as his identity as a student was implanted in her head by Neko's memory manipulation powers.
The robot reacted by saying, "You're too kind," to a supposedly invisible Neko (Kukuri couldn't see her). Later, it turns out that she isn't actually invisible. She just fiddles with the sensory perceptions of surrounding people such that they cannot see her. It doesn't work on robots, of course.
In episode 2, Shiro looks at a flyer with the name "Marilyn" on it and tells Kuroh that his imaginary sister is named Mari. His own name, "Yashiro Isana", was made up on the spot and is based on a poster he saw as well, detailing a certain Isana Shrine (Jinja, which consists of the same kanji as "Yashiro").
In episode 4:
The cleaning robot in Yashiro's room didn't recognise him as a student and tried to clean out the "trash". He's not a student and is absent from Ashinaka High's records.
The alibi photo which Kukuri found of Shiro had Shiro with his coat zipped up. He was trying to hide the bloodstains after Tatara Totsuka's death.
In CLANNAD, you will not be able to hear Nagisa's first line in the same way again when you watch episode 16 of the second series, and everything that comes after.
Nagisa: Do you like this school? I love it, very, very much. But nothing can stay unchanged. Fun things, happy things, all of these things will eventually change. Even then, can you still love this place?
In Murasakiiro No Qualia, the first few pages foreshadow the darker nature of the series, despite the lighthearted start.
Tenjou's claims regarding the frightening nature of Yukari's eyes and the perspective of the world that comes with them.
A minor (and perhaps easily missed) one occurs in Future Diary, showing the students with the top grades; Yukiteru, the main character, places firstnote thanks to his future diary giving him the answers to all his tests, and Yuno Gasai places second. In the Survival Game, they are designated the First and Second future diary owners, respectively.
Look closely at the first opening. It hints at all twelve diary holders identities, as well as who survives.
Listen to the lyrics of the second opening, which have extreme plot points inside its lyrics. Also, what's with all those blue characters? They don't survive the games, including the twelve diary holders, Yukiteru's friends, and 8th's orphans (whom are represented by burning candles, showing that she outlives them), and even Deus himself. Yukiteru, the winner of the games, is in color. Yuno, who regains her memory in her third body, and Minene, who survives through Deus's power but survives, are gray-scaled, because they lived on even though they lost the games.
In Attack on Titan, in episode one of the anime only, Mikasa is seen hauling twice as much wood compared to Eren, hinting at her vastly superior strength.
A subtle one is during training, Eren injures his head during 3DMG training. He recovers quickly (in one night!) and can be seen with small amounts of steam leaving his head. It's easily mistaken as a visual indication of his embarrassment and frustration rather than his Titan healing abilities manifesting.
In Kill la Kill, the on-screen reveal of Ryuko wearing Senketsu in the first episode is heralded by the song "Blumenkranz", which is later revealed to be the Leitmotif of the show's true Big Bad, Raygo Kiryuin, who, in episode 18, is discovered to be Ryuko's birth mother.
Throughout Satou Kashi no Dangan wa Uchinukenai Umino Mokozu insists she is a mermaid who must return to the ocean, after making a 'true friend', before an upcoming once-a-decade storm or she will die. The whole thing comes off as a metaphor. The needed a friend to help her escape from her abusive dad before it's too late. Alas it was too late in the end.
Mokuzu's name means "scraps of seaweed from the sea". It's an odd name and classmates even wonder what type of parent would name their kid such a name. It'd make sense for a mermaid at least.. Mokuzu's dad had been abusing her from infancy, to the point where she has a permanent limp due to a hip injury received as a baby and a broken eardrum which leaves her deaf in one ear. An abusive dad like him would be the type to name his kid such a name.
In the very first chapter, right after her introduction, she trips. Nagisa sees bruises under her skirt. A few pages later we see she walks with a limp, which she states is due to the witch that turned her into human.
Her father once wrote a song that no one remembers the last verse to. In that verse it turns out the man killed and dismembered his mermaid friend. Guess what he did to his daughter.