In episode 14 of Fate/Zero, Tokiomi mentions a treasure of Gilgamesh's he calls the "Sword of Rupture" which Gilgamesh is completely unwilling to use even though it could apparently easily destroy Caster's giant monster. In Episode 23 Gilgamesh summons it during his fight with Rider and completely destroys his Reality Marble and his entire army with only a few seconds of charging.
In the end of the Trigun anime, where Vash brings the Crossgun with him to the final fight, and leaves it rooted in the ground. He later interrupts Knives be lifting it from the sand created in their fight and shooting him up.
In the very first pages of Riki Oh, two guards chatter about how the eponymous protagonist has survived being shot five times in the chest when he sets off a metal detector.Fourty chapters later, the Big Bad of the current story arc shoots him with a sixth bullet which completes the "GNOSIS" hexagram, a seal that strips him of all his power.
In season 2 of Natsume Yuujinchou our titular Hero finds an ayakashi in his house, but he doesn't get rid of it because he finds out that it's harmless and can even prevent disasters from happening. To stop the tragedy, it must sacrifice itself. It did just that and saved Natsume from an evil ayakashi in the process. At the very end of the episode, he collects the remains of the small ayakashi saying that they're very precious to him.
Ouran High School Host Clubhangs a lampshade on this. The device that sets up the plot of the whole series is a large, expensive vase that will be broken. The vase is seen in the foreground of most of the shots leading up to the breakage...and is indicated by a large, blinking arrow. The blinking arrow returns in later episodes to point in every device and person whom will set the plot of the episode.
In Black Bird, Kensuke gives Misao a bottle of Whitesnake poison. This comes in handy when she's trapped alone with Soujou.
Naruto: The First Hokage's necklace that Tsunade gives Naruto becomes very important after the timeskip, as it becomes an essential instrument to control his Kyuubi powers.
When Sasuke's Team Taka is fighting Killer Bee, there's a rather prolonged focus on a tentacle of the Eight Tails that Sasuke had cut off. It later turned out that Killer Bee hid inside it while being underwater, while transforming another tentacle to look like his unconscious body, deceiving Sasuke into thinking that he had captured Killer Bee.
Itachi stuffed a crow down Naruto's throat, which comes out about 150 chapters later, and is revealed to be one of Shisui's Sharingan eye.
The cool space-time ninjutsu that Kakashi used in the Kazekage Rescue arc, appears again when Tobi is revealed to have the same ability, which also serves as a clue to his true identity.
The tablet hidden in the Naka Shrine is only readable with a Sharingan, and contains the reason for Uchiha Clan's creation (controlling the nine-tailed fox). It is revealed later that with a Mangekyou Sharingan and a Rinnegan, the full tale of the Sage of Six Paths and all the Tailed Beasts could be read from the tablet.
Edo Tensei was used by Orochimaru to resurrect the First and Second Hokage during the Invasion of Konoha Arc. It doesn't show up again for over 300 chapters until the Fourth Ninja World War arc, when Orochimaru's former Battle Butler Kabuto uses it on an enormous scale.
In the arc where Sai first appears, he refers to a dead brother. This is commented on quite a bit, showing Sai's lack of emotion and artistic ability. Much, much, much later, this turns out to be his Berserk Button, which is pressed by Kabuto in two ways.
Wendy Garret in GUN×SWORD carries around a gun given to her by her brother, Michael, when their home was attacked. It only has one bullet. There may as well be a large tag on the handle saying "FUTURE PLOT DEVICE".
In Yu-Gi-Oh!, if a character even explicitly obtains a given card (from a trade, a victory, or even just though picking it) rather than having it in their deck, it will be absolutely critical to their victory in at least one duel that season.
In episode 139 of the first series, Yami draws a card and places it on the field without looking at it, and Ishizu says that Yami knows the card is Fiend's Sanctuary. Yami's ability to predict and pull exactly the card he needs goes unnoticed until a hundred episodes later, when it's revealed how it exactly works.
Shortly before Battle City, Yugi trades a card while out with Anzu for a Trap called Lightforce Sword, which he later uses in the first duel of Battle City against the Exodia-using Rare Hunter and later against Strings, but after that, the card is not even mentioned again for thirty episodes when it plays a vital part of his duel against Kaiba in the finals of Battle City, saving him by delaying Kaiba from summoning Obelisk the Tormentor
Joey's Time Wizard! He's saved their necks with that card a lot!
The Deck Masters (Except for Joey's against the duel with Johnson) and some of the cards that Yugi and their friends (Specifically Serenity) during the Virtual World Arc.
Kuriboh actually helps save Yami Yugi from defeat, then, because of a card Rainbow Blessing, allows Yami Yugi to strike Gansley directly and win the duel.
The Dark Magician Girl helps Tea against by allowing her to summon Yugi's Dark Magician out of nowhere.
With Serenity, somebody who has never dueled before, she picks a card (St. Joan) thinking it looks cool. Combined that with her Deck Master's ability and with some help from Duke Devlin, her monster obliterates Nesbitt.
Kaiba's Lord of Dragon allowed him to summon a Blue Eyes White Dragon and obliterate Lector.
In Yu-Gi-Oh! 5Ds, the final Signer Dragon, Life Stream Dragon, originally appeared in one of Luna's dreams. It was finally unlocked by Leo from Power Tool Dragon late in the series.
In an episode Yu Gi Oh ZEXAL, Yuma uses Baby Tiragon to beat Cathy right one episode after he got it from Tokunosuke as the token of their friendship.
Early in the second season of Ghost in the Shell: Stand Alone Complex Togusa investigates the disappearance of a man who was last seen talking to people who have hired a number illegal immigrants as cheap laborers. It turns out he died in an accident while salvaging parts from an old nuclear power plant inside a restricted area. However, it's not a single episode about exploitation of refugees and endangering workersto save money, but kicks off the seasons main plot as the Big Bad initiated the illegal salvage operation to let plutonium fall into the hands of foreign terrorists to cause a massive scare against Chinese and Korean refugees.
A better example of a Chekhov's Gun in Negima is the bracelet that Ako won when she and Negi (disguised as Nagi) finished second in a pageant-like event during the school festival. Over a 150 chapters later, Ako is seen wearing the bracelet, with the item plying a key role in stopping a Magia Erebea-corrupted Negi from attacking her and the rest of the Sports Girls.
Spoileriffic example: Note Ku Fei's comment in panel five, then read chapter 311.
Way back in chapter 162, Chao brought her secret item, "Chao's family tree" that would indicate who will Negi marry in the future. It pops up again in chapter 349 (a copy of it at least) and this time, Negi's descendants are now a blank slate which means everyone gets a chance at being Negi's partner.
The most shocking Chekov's Gun is the truth about Poyo and Zazie Rainyday. For almost the entire manga, one of them is a background character with nothing interesting about them... unless you noticed what Zazie looked like on the two-page spread in the very first chapter of the entire manga!
One Piece is fond of this, though how critical the Chekhov's gun is varies per use. Among examples are a rather odd pinwheel worn in the hat of Genzo, the sheriff of Nami's home village. This pinwheel has three Chekhovs to its name. First, it inspires the attack Luffy uses to remove the villain-of-the-arc's giant sea cow from the fight. Second, along with Bellemere's tangerines, it forms the basis for Nami's new tattoo. But the true Chekhov comes at the end, when a flashback reveals that Genzo put the pinwheel in his hat to make the then-baby Nami laugh. To everyone's surprise, it worked, and so Genzo continued to wear it as a way of supporting Nami as she struggled, removing it only when Nami left with the Straw Hats.
The concept of Haki is a good example of this. In the very first chapter, Shanks is seen scaring a Sea King away simply by gazing at it. More than four hundred chapters later, the power is named but is not elaborated upon. Luffy is later seen unknowingly using a similar gaze on Duval's Bull, and it isn't until five hundred chapters in that the concept of Haki is fully explored.
In the Davy Back Fight arc, Luffy is outfitted with an afro, thinking that it will make him stronger in his upcoming fight. Then, at the end of the fight, a shard of mirror caught in the afro proves crucial to his victory.
Luffy's brother gives him a piece of blank paper early on in the Arabasta arc. The paper's purpose is left unknown for several hundred chapters/episodes (depending on whether you follow the manga or anime.)
The third movie has Usopp use an actual boomerang in order to attack the Big Bad, but as it turns out, it was fairly useless. However, it's later used to lure a bunch of Horn Eaters belonging to the big bad, by imitating a pair of horns, into a ravine, where they are trapped.
Oda seems especially fond of this trope. Early on in the story, our beloved pirate/clown Captain Buggy is looking for the treasure of one Captain John. A long long long way down the line during the Thriller Bark arc, Captain John's zombie turns up. After the conclusion of this arc, Buggy's self-proclaimed rival Luffy finds a cool armlet in the Thriller Bark treasure hoard, which stays with him for about forty chapters before he and Buggy end up in Impel Down together. Only THEN, do we realize that the armlet Luffy took is in fact the key to finding the long lost treasure that Buggy has been looking for all along!
One word: Laboon. The crew meets him just after they've entered the Grand Line, and it is mentioned that Laboon is waiting there for a pirate crew he befriended to come back. Several hundred chapters/episodes later, they gain a new crew member (Brook) who just happens to be the only remaining member of that pirate crew and his goal is to keep his promise that he'll come back to see Laboon again.
Even earlier than that, starting back in the Arlong arc, Luffy starts saying that their next crew member needs to be a musician. Guess which role in the Straw Hats Brook fills.
Captain John's treasure was predicted right after the chapter he picks it up at was released, so it wasn't a huge shock. Still the Captain John plotline is relatively low-key, but is probably another set up. When it was first shown it was just thought to be a random thing to let us check in on Buggy, and the real important event was Ace showing up on his ship. No doubt Oda is the king of this trope. Laboon and Crocus in particular have a lot of events connected to them. It seems everything after they arrive in the Grand Line has had some kind of purpose later on. The sheer impressiveness comes when you realize that some of these set-ups took more than a decade to complete.
Early on, we can see that some of the Arlong Pirates seem to have a second, sun tattoo in addition to the one that identifies them as part of the crew. Hundreds of chapters/episodes later one, it's revealed that this links to another, legendary pirate crew, the Sunny Pirates formed by Fisher Tiger from freed Fishman slaves with the aforementioned sun tattoo (actually a brand) being their symbol as well as a way to cover up the brand they received as slaves. The whole slavery angle ties in to the whole Fishman/Human racism dynamic that underpins the Fishman Island arc.
During a flashback in the Fishman Island arc it is mentioned that the Royal Family possesses a treasure capable of rapidly aging an individual. At the end of the arc it is revealed that the mysterious treasure was actually the Energy Steroids the New Fishman Pirates had been using to boost their strength. Once the effects wear off they are left decrepit and old.
In the title pages of most manga chapters we have sidestories depicting the adventures of Luffy's previous enemies after their encounter with the strawhats (Buggy, Hachi, etc.). If you still think that any of those are supposed to provide closure to those characters, then you didn't pay attention.
Air Gear has quite a few. See the series page for details.
In Blade of the Phantom Master, the main character attacks a gun dealer about half-way through the movie after he is shown a little gun designed for hiding in a sleeve, which he keeps after he tosses the gun dealer into the sea. Guess what the penultimate blow to the bad guy uses.
Pokémon Special gets away with this more often than is healthy for the reader's mind. Lt. Surge's gloves, the feathers on Yellow's hat, a shard of the Grand Meteor (multiple times), and the list goes on. Almost every object explicitly discussed in dialogue returns later in the saga — or even in a completely separate saga — to turn the plot around.
Couple this with the ridiculous amounts of Hilarious in Hindsight examples, and you can tell that Hidenori Kusaka is both 1: In direct contact with both Satoshi Tajiri and Junichi Masuda of Game Freak, and 2: An amazingly skilled mangaka who's only being held back by the Pokemon franchise's kodomo classification.
The anime gets away with this a few times too, the most prominent being in "Pika and Goliath" — Ash revealed he kept the Thunderstone he got all the way back in "Electric Shock Showdown" in case Pikachu changed its mind about evolving.
Ash won a King's Rock in a Pokémon sumo tournament in the Johto region and it was quickly forgotten. Fifty-three episodes later, Misty's Poliwhirl pulled the King's Rock out of Ash's backpack and it triggered its evolution into Politoed.
In the well-known deleted scene to the first movie, known as "The Birth of Mewtwo", we've got a serious . Amber reveals that Pokémon tears are full of life, and though it seems unimportant at the time, it becomes very significant when Ash is revived by Pokémon tears. "The Birth of Mewtwo" was cut from the English version, making Ash's revival completely ridiculous...
My daddy used to tell me a bedtime story that when Pokémon are sad, and they cry...their tears are filled with life.
Actually, even the dub includes a very subtle Chekhov's Gun for Ash's revival: When Officer Jenny explains the boat trip to New Island was cancelled due to the storm, the woman accompanying her addressed that cave paintings explained that several Pokémon died in a storm, and that the survivors' tears revived them.
In the same movie, when Brock sees the missing Nurse Joy poster, after remarking that she's cute, he realizes that he recognizes her. It's later revealed that she was in fact the one who summoned them to New Island in the first place, under Mewtwo's Mind Control.
Two in Pokémon Origins: the Pokémon Mansion (which contained information on Mewtwo), and the stones given to Red by Mr. Fuji (which allow Charizard to Mega-Evolve).
In Tsubasa Reservoir Chronicle, the eponymous reservoir, while it appears halfway through the story, does not seem relevant until the final arc, where a flashback and a reveal make it retroactively the most important location in quite possibly the entire CLAMP multiverse. Shoulda known CLAMP wasn't just throwing in random words.
Gankutsuou has many. One is a gun placed in a desk drawer by Fernand. The two suits of armor outside the Morcerf mansion are actually giant mecha. Then there's the watch given to Albert by The Count when they first met.
Stock in trade for Eat-Man, where Bolt Crank may spend the entire adventure snacking on a bag full of bolts and other small machine parts. At the climax however, he'll swallow the last bolt, then whip a BFG he'd just finished eating the last of.
Really, if he eats something at any point in the story, you can expect him to use it later, even if he obviously didn't plan to. For example, in one chapter, he escapes from being locked in a safe by eating the safe. Later, He's caught in a massive explosion... and survives by hiding in the safe.
There's also a subversion, during the MOLE arc. Early on, Macus is playing with a yo-yo and musing on how, in Zero-G, the yo-yo goes all the way to the end of its string regardless of what direction it's thrown. Bolt promptly eats it. Later, Macus has his legs cut off by lasers and is set adrift. Bolt whips out the yo-yo and sends it in his direction... But the string isn't long enough to reach him.
CLANNAD: Remember those orbs of light Miyazawa and the Girl in the Illusionary World were talking about? Those'll really come in handy muchlater.
A few times in Ranma ˝: the horned mongoose whistle Shinnosuke gave Akane ten years ago turns out to be the key to pacifying and sealing the Orochi of Ryugenzawa. The photo of Akane that Nabiki snapped (and tried to sell to Ranma, but was bought by Ryouga) gave him the impetus to save himself from a rockslide, and was later used by the bad guys to kidnap her.
Macross Frontier gets points for sneaking Chekhov's Gun into what looks to be a throw-away Accidental Pervert gag. The fact that the Vajra start retreating from Island 1 just after Ranka's scream in that scene is no coincidence.
In Sailor Moon, when Mako/Sailor Jupiter is introduced in the first season of the anime her rose-shaped earrings sparkle with reflected light. They seem insignificant until the beginning of the fifth season, when Usagi is trapped in Queen Nehelenia's illusions and loses the will to press on to save Mamoru and Chibi-Usa. When Jupiter shields Usagi with her body to block Neheleni'a lightning attacks one of Jupiter's earrings falls off and Usagi finds it later; the rose shape reminds her of her love for Mamoru, and she jolts herself out of her illusion to continue to save Mamoru.
Eureka Seven features a very sneaky Chekhov's Gun in the form of Eureka and Anemone's collars. They seem like random accessories until the very last episode, where it's revealed that they're devices meant to destroy the Scub Coral, triggered by Dewey Novak's suicide.
Kinda foreshadows its significance in episode 11 when Eureka does not take the collar off when bathing and episode 19 when the collar was intact while Eureka's clothes and hair were being consumed by the Scab Coral.
In Utawarerumono, Eruru wears an odd, apparently decorative loop in her hair at almost all times. Later it is revealed that it is some sort of transmitter originally made by the humans when it automatically opens the door to a human research facility.
The hollow mask that saves Ichigo during his second fight with Renji. Hanataro briefly brings it up before the subject is dropped for dozens of chapters. It is only brought up again with its meaning when Ichigo meets the Vizards and gains control over his hollow powers.
Ichigo's Super Hollow form in the Arrancar Arc could be this. They hint several times that the longer he stays in Hueco Mundo, the more power his hollow side absorbs.
The Fullbringer Arc is pretty rife with Chekhov's Guns, both loading and firing:
Chad mentions while in Hueco Mundo that his power is more like a hollow's than a shinigami's or a Quincy's. This is ignored until Fullbring abilities are explained to be due to coming into contact with hollows and surviving.
The substitute shinigami badge Ichigo was given at the end of the Soul Society Arc turns out to be way more than just a hollow-hunting license.
The source of Ichigo's Fullbring abilities gets explained in the Thousand Year Blood War Arc.
The dead Fullbringers turn out to be training in the Rukongai with the Shibas...
To top all of this off, Kubo promised that everything that has been left unanswered for the past 11 years of Bleach will be answered in full in the Thousand Year Blood War arc. Essentially, all of the secrets and questions that were left unsolved are all Chekhov's Guns. Revelations include the following:
The reappearance of the Quincy, seeking revenge for their disastrous war.
The reason Ikkaku and Renji have seemingly weak Bankai is that a damaged Bankai suffers a permanent power drain.
The King's Key which was Aizen's goal is revealed to be a special reiatsu imbued into Zero Division members.
The walls that fall to surround Seireitei came from the Spirit King's palace, which resides far above Soul Society, and the Shiba family's cannon is used to transport people there.
Kenpachi named Yachiru after the only person he ever admired, Unohana Yachiru, the first Kenpachi.
Rukia, Byakuya, and Ukitake all remark on Ichigo's striking resemblance to Shiba Kaien but then dismiss it as coincidence. Turns out Isshin was a Shiba, making Kaien and Ichigo first cousins.
Ichigo's inner Hollow insists repeatedly that he is Zangetsu and an integral part of Ichigo. Then it is revealed that the Hollow within Ichigo IS his true Zanpakuto and "Zangetsu" is the manifestation of Ichigo's Quincy power.
Magical Girl Lyrical Nanoha has Chekhov's Wave Motion Gun; an early episode in A's gives us an apparently throw-away scene involving a high-powered magical cannon, the Arc-En-Ciel. The Arthra is out of service most of the season being refitted. When it returns, what should it come equipped with, but an Arc-En-Ciel.
Oh please. There's another one which is WAAAAAAAAY back in season 1: Wide Area Search. Simple spell just to collect the magical jewel shards right? During the final battle, Nanoha used this again to track down Quattro.
In conjunction with the above spoiler, Season 3 (StrikerS) opens with Nanoha rescuing a girl from a raging fire and using Divine Buster to blow a hole clear through the entire building to get her out. That scene is nothing but Chekhov's Guns. The girl becomes Subaru, whose origins are crucial to the plot and lead you to one of the big Wham Moments of the season; and Nanoha stalls in a battle while doing Wide Area Search so she can stop Quattro, who when it is way too late remembers Nanoha has an attack that can also serve as the biggest Dungeon Bypass in history.
In Monster a hospital director helps himself to the unconscious antagonist's candy. Nothing happens for a while. And then they find his body next to a candy wrapper.
Detective Conan: It's frequently used and a regular watcher ends up being trained to look for them in every episode. They're particularly subtle, too. One episode involved the culprit wearing a headband with the name of her favorite singer. The singer, Okino Yoko, has an accent over the third 'o'language note This is also the spelling as used in The Other Wiki. Elsewhere it is just written as ou.. When the culprit committed the crime, blood, which was the same color as headband, got on it (conveniently right on the accent mark), and was discovered by Mouri *cough* Conan *cough* as the killer. If you are an American viewer, you might tilt your head at the odd spelling at first since, hey! You don't know how Japanese worth squat! It was probably caught easier by Japanese viewers, but still subtle, and no one really pays attention to it until Conan provides the proof.
In the Vampire Princess Miyu TV series, Miyu and Chisato purchase two good-luck charms from an artisan. The artist is a Shinma, and the trinkets keep Miyu from sensing Chisato's own energy, as she is an exceedingly powerful Shinma who hasn't been awakened yet.
Right before Lupin and Jigen are attacked in their room by the Count's assassins, you see Lupin fiddling around with some sort of forgery kit. What's he doing, you ask? Making the fake ring he gives to the Count about halfway through the film.
Near the end of the film, as the archbishop sent to marry Clarisse and the Count travels to Cagliostro, you might notice not only is the farmer who offers to show him a shortcut clearly Jigen in disguise, but the driver who arrives at the castle is not the same driver as when we first see the archbishop.
In The Mystery of Mamo, Goemon's sword is shattered in a duel and Lupin takes one of the shards. In the climax of the movie, Lupin uses the shard to save himself by reflecting Mamo's lasers back at him.
Griffith's Crimson Behelit in the Berserk anime. We first see it after the naked water fight that he and Guts have in an early episode, and apart from a different colored Behelit taken off a demon Guts kills in the very first episode, it doesn't have a lot of significance, save for Zodd's prophetic warning about how when Griffith's dream crumbles, Guts will face his death. The Crimson Behelit turns out to be the key to become the very next member of the Godhand, the Big Bads of the series, during the Eclipse, and when it activates, it's the point when everything goes straight to Hell for Guts and the Hawks that Griffith led.
Transformers: Robots In Disguise had a particularly impressive example. When the Decepticons were introduced, Scourge's protoform scanned a truck that Kelly was trying to escape in, and which Optimus Prime was holding up, meaning he simultaneously scanned Prime. Initially, the only outcome of this seemed to be a Decepticon who was ironically similar in appearance to the Autobot leader. Much later, it turned out that this event had given Scourge a hybrid Predacon/Autobot/human spark based on that of Optimus Prime, which in turn allowed him to control Fortress Maximus.
In Wind A Breath Of Heart, everybody has a special power. Except the protagonist. This point is made whenever the subject of the powers comes up, suggesting that the protagonist will eventually awaken to a kickass power. Oddly enough, the episode in which he uses his power was taken out of the TV broadcast.
In Mazinkaiser episode six, Boss gives Kouji a bar to protect him while trying to get to Mazinkaiser. Kouji accepts it, but points out he has protection in the form of his Photon Gun. In the next (and final episode), Mazinkaiser's steering wheel is destroyed in battle with Hell King Gorgon. As the machine tumbles back, the bar tumbles out and Kouji remembers Boss giving it to him, causing him to shove it in the shaft and finish the fight.
The sequel movie, Deathmatch! Great General of Darkness has an interesting one, though - way back in Mazinkaiser episode one, the titular mech thrashes an altered Mazinger-Z and it is never seen in the series again and it is never mentioned as to its fate. Come the movie, a knife Kouji uses to defend himself is revealed to be made from Mazinger-Z's remains!
Shakugan no Shana has a Chekhov's BFS, Blutsauger. It first appears in the hands of a minor antagonist, and when he's defeated, leaving the sword, any Genre Savvy person could correctly deduce that by the end of the season, it will be in Yuji's hands. Although it trades hands several times, Yuji does indeed use it in the first season finale, and in the second half of the second season he carries it regularly.
There was also the antifire ring, which shows up with the first minor antagonist and is given to Yuji afterwards. He uses it to survive two later fights, including the finale of the first season.
The tiny bombs that Sagara Sanosuke got from Tsukioka Tsunan in Rurouni Kenshin play an important role in the Kyoto Arc when Sagara uses them to blow up Shishio's battleship, earning a major victory for Kenshin and company.
The wedding kimono: Makes its first appearance in Episode 6, becomes a vital clue for the audience in Episode 18.
Revolutionary Girl Utena is mostly just clever storytelling and repetition so it's actual ChekhovsGuns are much harder to spot. Akio's planetarian is one of them, but a much more significant one is the Sword of Dios, drawn from Anthy's bosom every other episode. No one asks why. Come the second arc onwards swords are being drawn from everyone's chests. And, to cap it off, then the Sword of Dios has to be drawn from Utena's breast.
There's actually a fairly elaborate one in Tantei Opera Milky Holmes at the end of season 1. Mary and Kate from episode 5 inspire Milky Homes to not give up. Aileen from episode 4 gives the girls transportation to their final battle, the recurring Pig-Faced character comes by to deliver a Toys-Powered Ring from Sonya (episode 9) and a wedding plate from Claris (episode 6), Sherlock's various encounters with Henriette's Cleavage also come into play as well. The ring winds up saving Sheryl's life, the plate becomes crucial for Cordelia's defeat of Stone River, and Sherlock's previous brushes with Henriette ACTUALLY become a way for Milky Holmes to identify her as Arsene.
The mangaka of Aoi Hana and Wandering Son frequently includes characters that looks like they'll only appear once or twice, or that don't have much to them, that become important characters later on. Same thing with plot devices.
FLCL episode "Brittle Bullet". Ninamori receives a water pistol during the episode. At the end she uses it to cool off Naota after he's ejected from Conti.
Early in Princess Mononoke Eboshi warns that a wolf's head still has the power to bite, even after being severed. Guess how she loses an arm later?
Inverted in Yokohama Kaidashi Kikou — the story introduces tons of "unnecessary elements," never using them. This includes characters that are introduced but never meet each other, offers that are never used, and an actual gun that is never seen again after its introduction.
In Black Lagoon, the pistol Balalaika used to slay Boss Kousa and then threw into the ornamental pool is clearly shown to have a fingerprint on it, presumably Rock's from when she handed it to him. It's likely this will bite Rock later on in the series. Another additional meaning is to represent that Rock can never return to his home country, due to his status as a prime suspect in the murder of a Yakuza boss.
Yuuta's collection of items related to his "Dark Flame Master" in Chuunibyou Demo Koi ga Shitai!, which he originally planned on throwing away come tenth-grade, turn out to be useful whenever he has to distract and/or keep Rikka and friends occupied.
xxxHolic has the egg given to Domeki by Yuuko, who tells him that it'll be useful somewhere down the road. Subverted in that even though it's brought up regularly, the right time for it to be used never comes.
In the first volume of the manga, Watanuki finds Sakura's staff in the storeroom, and Yuko tells him it's just a plastic toy. Nope. That's the real deal, and it's extremely important.
Roughly a third of the way into JoJo's Bizarre Adventure: Diamond is Unbreakable, Rohan and Koichi wander into a section of town connected to the afterlife. One of the rules of this area is that when you enter or exit, you cannot look behind you or your soul will be taken away. After leaving that part of town, this fact is quickly forgotten about until the stand Cheap Trick attaches itself to Rohan's back. Just as it's about to kill him, Rohan points out where he's lead them to...
In Murasakiiro No Qualia, no one would have imagined the cellphone Hatou innocently wanted to buy would end up being used to re-attach her cut off arm and become a embedded means of communication with Yukari. But that's not where its usefulness ends. It also becomes the means through which Hatou can interfere with the parallel worlds by communicating with her alternate selves.
In YuYu Hakusho, Koenma's pacifier which is even referenced during the Dark Tournament Arc as being significant in an off-hand scene with Koenma and Ogre. It turns out to be an artifact to create a nearly unbeatable barrier that Koenma tried using on Sensui.
In Tiger & Bunny, while getting annoyed at Kotetsu's attempts to get him a birthday gift, Barnaby randomly points to the television show that was advertising a rare diamond necklace and says to get him that. Later on the episode, a gang steals it and Kotetsu catches the boss and presents him to Barnaby, complete with the diamond necklace.
Kotetsu's nickname of "Bunny" tends to aggravate Barnaby to no ends. In episode 23, Barnaby's memories return when Kotetsu uses it.
At the beginning of the Monkey Hunter arc of Gintama, Gintoki ends up getting his...joystick turned into a hexagon screwdriver, which ticks him off to no end, partly because of how rarely one would ever need such a screwdriver. Come the end of the arc when he confronts the aliens responsible for the deed, it turns out the only thing that can stop their ship's engine is precisely that. The scene is about as awkward as one might imagine.
There are a TON of these inBlack Butler. Most of them overlap with one of the subcategories of this trope, except for the pairings in chapter 71 of the manga, and several examples from the anime.