AIR has a crow (raven?) that is introduced early on and inconspicuously follows the main characters around throughout the first 3/4ths of the show. After the show invokes Anachronic Order, the story starts over from the beginning focused around the crow, a reincarnation of Yukito named "Sora", and his instrumental contributions to the plot.
In Ao No Fuuin, Soko's older brother is introduced along with her family and appears as nothing more than a slightly aloof older sibling who goes to college and later dies in the explosion resulting from a bomb sent to their home. Presumed to be dead, he is not seen for several chapters and finally returns, revealing himself to not just be alive, but also be the Genbu of the northern Family intent on protecting Soko and basically becomes the Big Bad of the series.
Ymir is introduced along with all the other supporting cast, but her name is not given until Ch. 37. She's an independent Titan Shifter, and over 70 years old.
Krista is the sweet girl everyone adores, but seems incredibly minor right up until we learn that she's actually a Heroic Bastard. Her family's influence is such that both factions want to obtain her, as she has the right to learn the secrets of the Walls and the authority to reveal them to outsiders.
Azumanga Daioh's Kagura makes a few appearances before her introduction, the most notable of which is in the first sports fest.
Kagura gets a little weird here. She appeared in the manga a few times before joining the main cast too, but the anime expanded on how often she made appearances a good deal.
That's because the anime mixed up the order of a few events, like the pool episode, so that they came earlier.
That young, redheaded train conductor from Baccano!! doesn't seem remotely important at first. He's just a Red Shirt whose only distinction is being the first to be killed on the train, right? Er, not quite. In episode nine we learn that neither of the corpses that Jacuzzi found were his — they were his victims'. Conductor guy turns out to be the Rail Tracer that has been picking off the Lemures and White Suits throughout the series. And that's not even half of it...
And then the man in the trenchcoat in the scene where Isaac's ear gets crushed is is the Martillo Family's Ronnie Suchiart, aka the devil from the Advenna Avis. He plays a larger role in the light novels.
And Fermet, the man that tortured Czeslaw into nigh-sociopathic paranoia? Turns out he's the series's Big Bad.
Zigzagged in Berserk. Since the manga starts off as an In Medias Res, Puck is introduced as a primary character in the Black Swordsman arc. After the Black Swordsman arc is over and the story switches to the Golden Age Arc - which is a flashback - Puck has not been introduced. However, after Guts and Casca are rescued from an ambush by the Blue Whale Knights of Tudor, Judeau gives Casca a bag of elf dust, saying that an elf he used to know while traveling with a band of performers gave it to him as a gift. The elf in question is indeed Puck, but he is not referred to again until the events of the Eclipse, in which Rickert, who was left behind during the Griffith rescue operation, was traveling with the same band of performers that Judeau accompanied in the past, with Puck still in their presence. After the two year time skip at the beginning of the Conviction Arc (which the Black Swordsman Arc overlapped chronologically) Puck is presented as a larger character.
Snake wanders off at the end of the circus arc. He is responsible for one of the deaths in the Murder Mystery arc, and eventually becomes a secondary character.
In the anime, Ash is first seen as Queen Victoria's nameless escort/servant during the Curry Contest.
Also in the anime, Lau, the comic relief and exposition character, eventually becomes a formidable villain.
In an early story arc of Blade of the Immortal a character is introduced, but disappears at the end of the arc with their story apparently self-contained and complete. Many, many volumes later, guess who shows up at the side of Shira? Kawakami Araya's son Renzo.
The chapter 1 title page shows several people in the background. Almost all of them are introduced shortly afterward as Ichigo's classmates and most have only a minor role in the manga. However, one character in the group remains anonymous for nearly 200 chapters: Shinji Hirako, who becomes a major character but only in the third story arc.
In chapter 7, Ichigo's dad Dr. Isshin Kurosaki is on the phone with the local hospital demanding they open up beds for patients he cannot treat in his tiny clinic, which he says the director of Karakura General will do as a personal favor. That director is Dr. Ryuuken Ishida, Uryuu's father, a Quincy, and Isshin's longtime friend. All of this occurs long before Uryuu (a far more important character) enters the story. The Odd Friendship between Isshin and Ryuuken isn't revealed until chapter 241, and even then, its significance is only explored in the final arc of the story, more than 500 chapters after Ryuuken is first introduced. And Ryuuken's relevance is in direct proportion to the earliness of his introduction: a small miscalculation on his part sets up the main plot by throwing Masaki and Isshin together.
In chapter 27, the beginning of the Don Kanonji story, a figure in the crowd note on the page where Rukia starts doing Don Kanonji's signature BOHAHAHAHA laugh looks distinctly like Uryuu, who will not be introduced until the beginning of the next story in chapter 33. In chapter 29, a person is seen moving toward the roped off area where Don Kanonji's exorcism is turning a soul into a hollow, but they stop because Ichigo jumps over the rope first. As Ichigo goes past, the person's back is clearly visible (but their face is not), and the clothing and hair look like Uryuu. Word of God later confirmed that Uryuu was ready to intervene if Ichigo hadn't been on the ball. In the anime, Uryuu also gets a brief cameo in a general classroom shot in episode 7...and sure enough he's doing embroidery.
In chapter 56, Byakuya tells Rukia he understands her desire to protect Ichigo because of Ichigo's resemblance to "him". Although this is an obvious reference to Kaien (introduced 77 chapters later), it also sets up Hisana's story (123 chapters later) which proves Byakuya told the truth: he really does understand the desire to protect someone who resembles a loved one. Not only that, but the chapter's cover image initially appears to be a dead or unconscious Rukia with oddly shaggy hair. Hisana is almost identical to Rukia but with a longer, rougher hairstyle and her introduction cues a reinterpretation of the picture in Chapter 56 as Hisana, not Rukia.
At the end of the Soul Society arc, Aizen leaves Seireitei via negaccion and the shinigami left behind observe that there's something in the garganta behind the gillians, the only sign of which is a giant eye. Hundreds of chapters later during the battle for Karakura Town, Wonderweiss appears with his giant pet, Fuura, a misshapen being with one giant eye and the ability to destroy Yamamoto's flames that are trapping Aizen. It's revealed Fuura was the creature that was hovering behind the garganta at the end of the Soul Society arc.
After Grand Fisher's defeat, he's seen talking to two other Hollows in chapter 25. One of these is Di Roy Rinker, who next appears in chapter 199 as one of Grimmjow's Fracción. The other is Aisslinger Wernarr, whose next appearance is chapter 241 in the first fight in Hueco Mundo.
In the sixth episode of Blood+, the heroes go to the enemy's laboratory to save George. While there, David checks a computer and remarks that there is no information on it about "Diva", who is referenced several more times before it is revealed that she is Saya's Evil Twin and the Big Bad.
In A Certain Magical Index, Saten and Uiharu appear in the opening credits of the first season. Neither appear in the actual show, and only debut in the spin off, A Certain Scientific Railgun. Uiharu does appear in Index later though. In the second season, two years later.
Kuroko also makes an early appearance in episode 2, while she only makes her official debut in episode 10.
In Code:Breaker, Aoba. She is Sakura's best friend, and apart from that, just an attractive female character. She later is discovered to be Code:Revenger, one of the top agents of Eden.
Code Geass had Schneizel make an appearance at Clovis's funeral at least a dozen episodes before he actually enters the story.
Also had Mao appear early in both episode 12 and 13, even though he's not officially introduced until episode 14. In hindsight, though the first cameo becomes pretty damn significant as it explains how the hell Mao knew Lelouch was Zero, knew C.C. was with him, knew Shirley liked him, and knew her father was killed by Zero, all of which become important parts of his Batman Gambit.
The first shot in the first episode of Darker Than Black shows a girl in a white dress standing at the edge of a lake and looking at the stars. This isn't given any explanation, and as the scene immediately cuts to a Batman Cold Open, viewers are likely to ignore it... until episode 11, when Hei starts panicking when he sees an illusion of her in the Gate. Turns out she's his dead little sister: a Person of Mass Destruction, the reason for the Heaven's Gate explosion, and the reason for both her brother's powers and his personality.
In Death Note, Light goes through a period of dating other girls much to Misa's chagrin. We get a good look at one of them, Kiyomi Takada, who shows up again near the end of the series and proves pivotal to Light's defeat.
You know those namelessextras standing around in the background of Episode 23? Turns out that a good portion of the plot hinges on their presence.
In the pilot, Miura is first shown being questioned by the police. Much later, when main character Taro Kagami gives up the notebook, more people get killed, including the detectives, and Miura is the second Death Note user.
In the "Distinguished Family's Consecutive Accidental Death Case", Conan sees a familiar man in the Osaka Police, but he didn't recognize him at first. He is Heizo Hattori, and he's an old friend of the Chairman in the case and almost immediately afterwards, Heiji shows up, revealing that he is his father.
In another case, Conan takes care of a toddler while his widowed mother goes to find Kogoro after she's being followed around by a mysterious figure. That little boy is Santa Ishikawa, and he turns out to be the key to solving the case.
Kamemon in Digimon Savers. All he does is silently wander around DATS headquarters serving tea, until it turns out he's just shy, and is actually the Digimon partner of Yushima, local head of DATS and the Cool Old Guy who randomly shows up to give Masaru advice. Even after that, he and Kudamon are revealed as agents sent by Yggdrasil to spy on humans. Doubles as Let's Get Dangerous! when he gets to show off his later evolutions, Gawappamon and Shawujingmon.
In the D.N.Angel anime, Krad is shown in the very first scene (even giving the first spoken line!), but doesn't get a proper introduction until a few episodes later. (And in the manga, his introduction was delayed even more.)
In prequel to Dogs: Bullets & Carnage, during the first story that introduces Mihai, there's a panel showing a red haired guy with an eye patch trying to get past him and get out the door. Guess who's introduced as the subject of the next story?
In Dragon Ball, Kame Sen'nin's first appearance doesn't amount to much. He happened to have a Dragonball and he gives Goku the Kintou'un. His next appearance he's revealed to be the Muten Roushi and the trainer of both Gyuu Maou and Grandpa Gohan. After that he plays a major role training Goku and Kuririn. Sadly, he was Demoted to Extra by the Majunior saga and it was just downhill from there.
Chichi's an even better example. She first appeared as a minor character who had a crush on Goku, and in the manga after her first appearance she was never seen nor mentioned again until the 23rd Tenkaichi Budokai twelve volumes later where she's reunited with Goku and they wind up getting engaged. The anime screwed this up however by having her appear every now and then in a couple filler episodes.
Eyeshield 21: Kongo Agon, one of the most memorable antagonists in the series makes his debut appearance watching the Devil-Bat's second ever match. Later on, while trying to find and recruit Musashi as a kicker, the Devil-Bat's run into Kotaro, who becomes their last opponent in the Tokyo Tournament. Than during the opening of the Kantou Regionals, Sena is approached by Reiji Marco who plays quarterback for the Hakushuu Dinosaurs, and wants to know if Sena would like to trade opponents (upon finding out Sena will be facing Agon he backs off); he seems like something of an afterthought compared to some of the other players there, but he and his team end up being the Climax Bosses of the arc.
Maruko "Marco" Reiji, quarterback of the Hakushuu Dinosaurs, is introduced at the beginning of the Kantou arc as a smooth, though somewhat cowardly player. Later on, his team becomes the final and most challenging opponent the Devilbats face in the Kantou Tournament.
Not to mention Musashi, the player who won the Christmas Bowl for the Devil Bats, who was originally introduced as the no-name carpenter working on the team's club house long before it was revealed that he was one of the founding members of the Deimon Devil Bats.
The Ha-Ha Brothers, as well, were originally the nameless bullies tormenting Sena in the first chapter before disappearing for some time and eventually being pressured into joining the Devil Bats as offensive linemen during the game against Zokugaku.
The manhwa Faeries' Landing has quite a few characters that do this and later become important
In the Fairy Tail manga, before they are officially shown in the manga during the Oracion Seis arc, the Stellar Spirit twins Gemi and Mini are visible on two chapter cover arts. Given that it's done by Hiro Mashima it's possible that he drew them at random and decided to make them Gemini later.
Ur also counts as she was said to be alive at the end of the Galuna Island as a part of the ocean. Arcs later, Ultear falls into the sea and into her mother's memories, which is what convinced her to Heel–Face Turn.
Also, all the members of Oracion Seis (except Brain) are visible as unnamed child slaves during Erza's flashbacks of her childhood.
Selim, son of King Bradley in Fullmetal Alchemist. Seems like a harmless kid, but later revealed to be the most dangerous Homunculus of all seven, Pride.
In a more minor example, with more immediate payoff, Roy Mustang is initially introduced in Chapter 4 of the manga as seemingly nothing more than an extra to set the scene for the current story, before being revealed as a major character at the end.
In the chapter with Winry arriving at a train station, Izumi and her husband can be seen in the bottom right of a panel perusing the timetable. When they both arrive later, the author even puts a little footnote that encourages the reader to check back in the earlier volume.
Probably the most extreme example would be the Gold-Toothed Doctor, an unnamed alchemist that shows up very irregularly.
Kimblee shows up for a short aside really early, but isn't seen until something like three years later (in real life time). A lot of people don't realize how long a gap there is, because he escaped from prison and was much more active much earlier on in the 2003 anime. That, and he showed up in the flashback volume of the manga, before he was released from prison. Arakawa was clearly itching to get to him.
The 2003 anime version is fond of this trope, bringing back characters from the beginning of the series who seemed like Filler Villains as important characters towards the end.
Selim is this in the 2003 anime too; the difference is he ends up being directly responsible for Mustang beating Bradley.
And let's not forget the even more minor Lyra, who appears in episode 4 of the first anime as Yoki's assistant and later has her body stolen and becomes host to the biggest of the Big Bad's.
Episode 39 of Futari wa Pretty Cure features reappearances by all the minor classmate characters up until then... along with Yui, whose debut episode was number 43. Episode 44 then gave a brief cameo by Chiaki, just before her starring role in episode 45.
Chapter 14 of Gakuen Babysitters mentions by name the strict high school chemistry teacher, Hebihara, who's known for being strict and overworking. 11 chapters later, he's revealed to be the father of Kamitani, one of the supporting characters.
In the first chapter of Get Backers, there's this snotty brat who shows up when Ban and Ginji are ten yen short of the fee to get back their recently-towed car. He says he'll give them ten yen if they retrieve his Final Fantasy game, and they end up getting beat up and never think about it again... until volume 14, when the exact same thing happens, and Ten Yen-kun turns out to be a missing kid that our heroes will be hired to "get back" later that day.
The first is Tetsuya Kouji, whose mech gets blown to smithereens in episode 1, leaving him in the hospital for most of the series. He shows up as a Big Damn Hero in the last arc.
The second is Anna's missing father, who is mentioned in an early episode and then pretty much does the same thing as Tetsuya is the final arc. And the kicker? This is a double example, since he was also the priest performing the main heroes' wedding in the first episode.
And then there's Ribbons Allmark. He spends season one as Alejandro's quiet minion, then backstabs him in episode 25 and takes over his role as the Big Bad for the rest of the series. Yup, fucking ribbons indeed....
In Hajime no Ippo we're introduced to Yamada Naomichi, a weighty, timid young man who admires Ippo. Yamada trained in Ippo's gym for several months, and became a pro boxer before moving away, and we sort of forget about him after that. Two years later, he returns as 'Hammer Nao', Ippo's opponent for his second title defense, with a shaved head, scary demeanor, and lost enough weight to end up in Ippo's weight class, and everyone lampshades this drastic change.
In Haou Airen, a kid named Kaafai gets an unwilling first row view of Hakuron raping his own girlfriend Kurumi, whom the poor kid had befriended. Guess who, in the last volume of the manga, ends up shooting Hakuron dead?
Schrödinger in Hellsing appears relatively early on in the manga and OVA series, and has the interesting but passingly mentioned ability to be "everywhere and nowhere". His ability comes into full effect in the final volume of the manga, where he commits suicide and allows his body to fall into the river of blood Alucard is absorbing. The Major explains that Schrödinger's ability depends on his ability to perceive himself as an individual; if he becomes one of the many millions of souls within Alucard, however, he is unable to distinguish himself and is thus unable to truly exist. This quandary, in turn, causes Alucard to cease existing in the real world, which was the Major's Evil Plan all along.
Hidamari Sketch: The two new tenants of the Hidamari Apartments, Nori and Nazuna, were de-Faceless Masses-ized among other admission exam takers in the second season OVA. They were actually introduced in the second episode of the third season.
Akasaka from Higurashi: When They Cry is introduced as a minor character in the first season, only interacting with Rika, who discusses with him his wife's death and how to save her. In the second season, he plays a much bigger role, saving Rika from the Yamainu and Takano multiple times.
Inukami!: There's this kappa that hangs out in the background for a few episodes. In the climax he saves Keita's life.
Jojos Bizarre Adventure plays with this by having two Stand users targeting Jotaro's group mug an "unimportant, annoying faced man". At the end of the episode, the man has a bunch of hired thugs beat them up and hospitalize them before Jotaro's group even realizes they were under attack.
In a later episode, Hol Horse uses his Stand to shoot off the ear of a man who tried to take his cab. The man sees him again while in a truck driven by his friend, and they attempt to run him over but accidentally crash into Jotaro's group instead.
Mishio in Makoto's arc of Kanon, and in the Kyoto Animation version, all the major girls.
A major antagonist in Katekyo Hitman Reborn! largely responsible for the hunt on the hero's family (and the hero's death-in-the-future) is revealed to be Irie Shouichi, a seemingly random kid who appeared in one chapter to be traumatized by the wacky antics of the hero's familyfourteen volumes ago.
Subverted now, since it was all a very, very complicated Batman Gambit, co-produced by the allegedly deceased hero himself.
But now you have the even more inconspicuous Kawahira-ojisan who was only mentioned in passing by I-pin OVER 20 VOLUMES AGO as a man she DELIVERED RAMEN TO!
Sai, Kaede, Madoka and Arisu from Kidou Tenshi Angelic Layer. They don't have as big of a role as most examples, though, save Sai, although Kaede does make an appearance in Chobits(dead).
In King of Thorn, the Big Bad, Zeus, names an brief unnamed appearance in Volume 2 of the manga as a security administrator.
In K-On!, Yui can be seen running past Ritsu, Mio, and Mugi on her way to school in the first episode before they all are introduced later.
Kyouran Kazoku Nikki features an odd girl with pink hair dressed like a butterfly who can often be seen in the background for the first 12 episodes. Then comes episode 13, where she is finally introduced: she is Hiratsuka Raichou, considered by Ouka's Supernatural Phenomenon Treatment Bureau to be their biggest mistake and "The Empire's biggest traitor". Despite this, she has somehow become the Head of the Bureau, and is therefore the person in charge of "Operation Cozy Family", with all signs pointing to her as a future Big Bad.
In the first episode of Love Lab, Natsuo mentions Suzune, a shy and rarely-seen girl who acts as her secretary. At the end of the episode it turns out that Suzune has been watching Natsuo and Riko the entire time.
In Magic Knight Rayearth, the girls are given a seemingly pointless "mascot", Mokona, to accompany them on their quest. In the second series, it is revealed that Mokona is literally God.
Pointless? How many other mascots are both a Bag of Holding and a camper, all in one?
The first time Evangeline is mentioned, it's in a note written by her picture in the class roster. Two volumes later, she appears again as the manga's first real antagonist. A few volumes after that she saves Negi's butt during the Kyoto arc. After that, Negi eventually begins training under her. She is one of the most powerful mages in existence, after all.
Takamichi is introduced as merely the teacher that Negi takes over for. Turns out he's an extremely famous mage, and exceptionally powerful combatant who knew Negi's father. There's also a few panels of him transporting into Mundus Magicus. This isn't mentioned again until 70+ chapters later.
Chao Lingshen. Yes, merely saying the name is a spoiler. First seen hawking her restaurant's food in the first chapter of the manga, she goes on to be the Big Bad of the Mahora Festival arc. She's also Negi's descendant.
A picture of Ala Rubra appears as early as chapter 53. In it, of course, are Jack Rakan, Albireo and Zect. Plus Takamichi's mentor Gatou. We still don't know what's up with that guy, only that he taught Takamichi and Asuna kanka and erased Asuna's memory. Right before dying, which is his exclusive domain in this series, even in flashbacks.
Zazie in one of the earliest artworks is dead center with claws for hands. Cue the least development of any character and all of ten lines in the series until almost 300 chapters later she appears in the middle of the Magical World. Bricks were shat; lampshades rained from the skies. And it was actually her identical sister who's also a demon queen. Not long after, in Mahora, Zazie starts talking.
The main character of Mai-HiME, Mai, is conspicuously absent for most of Mai-Otome, which features almost all of the characters from the former. She only shows up a couple of times: once on a poster in the background of a shot, and as a silhouette during a narration of her untrue tragic backstory. She shows up in one of the last episodes and becomes a key character in the final battle. Subversion: Tate (Mai's love interest in Mai-HiME) also appears as a silhouette during said backstory, but the story isn't true after all and he never actually shows up or becomes important.
Mobile Fighter G Gundam: If you thought that Michelo Chariot and Sir Gentle Chapman were one-time rivals for Domon Kasshu... boy, were you wrong. Michelo joins the Devil Gundam group and later Gentle Chapman is revived as a DG zombie by them.
In Monster, Johann and Anna Liebert are briefly shown on Tenma's TV as the children of a foreign trade adviser who successfully managed to flee East Germany.
In Muhyo and Roji, a girl is briefly shown asking Enchu, who is busy studying, to play with her, Muhyo and Yoichi. The girl appears again in a later arc and turns out to be Yu "Biko" Abiko, one of Muhyo's old friends and a major ally.
Naruto has Shisui Uchiha, whose only initial purpose is to be the person Itachi killed off-screen in order to gain the Mangekyo Sharingan. Over 200 chapters later, we learn that Danzo stole his Sharingan eye.
Later on it's revealed that after his eye was stolen by Danzo, he gave his other eye (a Mangekyo Sharingan) to Itachi Uchiha after using genjutsu to make it appear as if he had destroyed it, then he died in order to allow Itachi to awaken his own Mangekyo Sharingan.
The entire Team Minato, but especially Obito and Rin. The team first appeared in the title page of Chapter 16 of the manga, which shows Kakashi in bed with two picture frames, one of his current team and one of Team Minato, which he was in as a kid. While it was known that Fourth Hokage, his sensei, sealed Kyubi into Naruto, we don't see Team Minato team in action until chapters 239-244 of the manga and episodes 119-120 of Naruto Shippuden. Obito's main importance was that Kakashi inherited both the Sharingan and his present-day behavior and ideals from him, while Rin seemed to be there just to fill the chick role of the trio and further the Generation Xerox comparisons with Team 7. Flashing forward, we find out that Minato is actually Naruto's father, that Rin was killed by Kakashi, which actually was what caused Obito to turn into Tobi, the Big Bad of not only the second half of Naruto, but arguably the entire series - in fact, her death is pretty much the catalyst for almost every major event in the story. Chekhov's Gunman Squad if there was one.
Tobi initially was simply a goofy member of the Akatsuki. Later, we find out that he is its true leader, and is also Madara Uchiha, though as mentioned above, he's actually Obito Uchiha.
At the end of part I, Sasuke explains to Naruto during their battle that the Final Valley was created when the First Hokage fought his best friend who betrayed him, such is the explanation as to why there are statues of them there. Way late into part 2, we find out that said best friend was Madara Uchiha; while he is not Tobi, he is one of the main villains, being the person who was responsible for corrupting Obito and coming up with his Evil Plan to begin with.
In the first episode of Neon Genesis Evangelion, Shinji sees a vision of Rei in the city before she's even introduced.
Kaoru Nagisa appears in the OP of every single episode, but goes unintroduced until episode 24.
From the anime's very first run in 1995, Toji's sister was The Ghost that was mentioned a grand total of two times. Then came Rebuild 2.0 in 2010 where she appeared for the first time on-screen for a few moments, upped by 3.0 two years later where she gets a name (Sakura) and becomes a secondary cast member. That's a total of seventeen years between first mention and first appearance.
Mihoshi from Nichijou is initially presented as an unnamed, annoying kid riding in the same train car as Yūko. It isn't until the end of the sketch that we learn that she's the younger sister of Misato, one of the show's major characters. From then on, Mihosi becomes a fairly prominent supporting character, and is even added to the opening credits for the latter half of the series.
One Piece is chock-full of these, given that Oda planned the whole story from the start and had all characters ready in place since he planned One Piece to last only five years, only to find himself enjoying it too much and having far more support than he imagined. People that were chilling in the background or just mentioned in passing will turn out to be vitally important to the plot. During a battle, Buggy the Clown relates his relationship to Shanks in the form of a flashback, and it opens with an argument between him and Shanks being broken up by the ship's first mate, who appears in two panels and is not mentioned again. Almost 500 chapters later, we learn that this man is Silvers Rayleigh, who is both the man that the Straw Hats need to alter their ship for undersea travel, and the former first mate...of Gold Roger!
Almost equally sneaky is the Laboon arc. The Straw Hats end up meeting a depressed whale the size of an island, and Crocus, the old man who takes care of the whale. We find out that Laboon's depression comes from the fact that his old crewmates left him and never came back. It's assumed that they all died or fled the Grand Line. As we learn in the Thriller Bark Arc, the entire crew did die. However, one of them came back, courtesy of the Yomi Yomi no Mi (Revive-Revive Fruit). This Devil Fruit revived Brook, the one who was closest to Laboon out of the whole crew, as an afro-sporting skeleton, whose only remaining purpose in life is to fulfill his promise to Laboon, which leads to him joining the Straw Hats.
Crocus also has some hidden depths that are revealed a bit later; he stated that he was a ship's doctor in the past, and his last line as he watches the Straw Hats sail away heavily implies that he knew Gold Roger. Putting two and two together is quite simple here, but to go into more detail, Rayleigh reveals that Crocus journeyed with them for three years, with the goal of locating Brook's crew, to keep Roger's illness at bay. These major points are just a few of the big problems with 4Kids' choice to cut the Laboon arc out of their dub of the anime.
Oda loves these so much that he might even be sleeping with them. A presumably bad Marine official that was introduced in Koby and Helmeppo's Chronicle of Toil, was many chapters later shown to not only be the person that cornered Gold Roger several times, but also Luffy's grandfather. Then there was the mysterious Dragon that helped the Straw Hats in chapter 100; he was later revealed to be a famous revolutionary and (much later) Luffy's father.
Coby and Helmeppo themselves qualify. They were introduced in the very first arc, and came back almost 450 chapters later after they Took a Level in Badass.
In the beginning of the Arlong Arc, Jinbe, one of the Seven Warlords of the Sea was mentioned. This was in 1999. He made his first appearance in the Impel Down arc. In 2009. Finally, in 2011, he's fighting alongside the Straw Hats in the Fishman Island arc, and as of the end of that arc, it's pretty much guaranteed that at some point in the future, he's going to be joining the Straw Hat Pirates.
On Jaya Island, three men appear causing trouble around a town. Not only are they part of the Blackbeard Pirates, an incredibly powerful pirate crew, the random bar patron that Luffy almost got in a brawl with is one of the series' Big Bad.
Nami is seen in the first episode of the series, but isn't introduced until the Buggy the Clown arc. She's also in the very first color spread in the manga, before either she or Zoro appear in the story.
When fighting Zoro, Hatchan mentions that he's the second-best swordsman on Fishman Island. Five hundred chapters or so later, we meet the best Fishman swordsman at Fishman Island, who's been hired by the Big Bad.
After Thriller Bark, the Risky Brothers tells the crew how mermaids' beauty on Fishmen Island even made the Pirate Empress Hancock jealous. Mermaids and Hancock are both introduced in the following few arcs.
Even better, it's later revealed that the Mermaid Princess has a special power that can potentially destroy the world. It turns out that one of the ancient Weapons Of Mass Destruction, Poseidon, was actually the previous Mermaid Princess, making the current one the reborn Poseidon.
Buggy the Clown tends to drop in once in a while just as the audience has forgotten about him. He's one of the early Big Bads, giving Luffy an actual challenge due to his countless knives and Devil Fruit powers. At the end of the first saga, he comes back for an attempt to take revenge on Luffy, only prevented from decapitating him when he is struck by lightning. He follows Luffy to the Grand Line, appearing now and then. In the Impel Down arc, he's forced into an Enemy Mine with Luffy. He serves mainly as comic relief, but once
During the Jaya and Skypiea arcs, we learned about Montblanc Noland, an adventurer from 400 years ago. It was briefly mentioned that, among his many adventures, he had visited an island populated by tiny people. About a decade later, in the Dressrosa arc, Robin and Usopp are kidnapped by the Tontatta tribe, a race of tiny people. Usopp notices that they have a statue dedicated to their greatest hero, Noland, and gets out of imprisonment by pretending to be a descendant of his.
During the Dressrosa Arc, Sabo makes a reappearance. The significance here is very dominant: this person appears after the databooks had confirmed he was dead!
In the Fishman Island flashback, Fisher Tiger rescues Koala, a little slave girl, and takes her home. But not before spending time with the Sun Pirates. After she arrives home, her parents try to tell her that "Fishmen are bad" and all that. Cut 12 years later (in-universe time) to Dressrosa, where we see Koala is not only a member of the Revolutionary Army, but a master of Fishman Karate.
A very well hidden one is found on the cover of chapter 691, which is dedicated to One Piece Film: Z. Among the dozens of young Marines on the cover is one in particular, hidden behind Nami's Clima-Tact. Waaay later, in the Dressrosa arc, said Marine makes an actual appearance; it's Corazon, Law's care-taker and dear friend.
Years ago, there was a little girl who played in the rain and she once saw a pre-teen boy and she tried to talk to him, but he ran away. That young boy's name? Takehiko Henmi, the tutor and stepbrother of the aforementioned girl, Nanako Misonoo.
There is a pretty maid who is given the job of cleaning Fukiko's old room in her summer mansion. That woman is Minako, who is the maid in said summer home.
In the first chapter, the protagonist meets a mysterious girl who speaks of him as though she knows him. That turns out to be the Intention of the Abyss, though it's unclear if she was talking about him as a rabbit doll or when he was Jack.
Later, in the fourth chapter, a mysterious man behind a curtain speaks to Oz. Guess what? He reappears many times after that, It's Jack Vessalius, the hero of Sablier that resides in Oz's body.
Another example has to be when Glen is with Oz down in Sablier and looking at him that a random flash of a girl with long hair who looks like Alice appears. You can't see her face, just her hair and her bottom features. She appears in Glen's memories....As it turns out, that young lady is Lacie, someone who is indeed verysignificantintheplot.
Lastly, when Jack tells Oz he has the right to use Alice's powers, a lot of times a rabbit doll appears. Later on, we learn that doll is Oz.
Paranoia Agent has Lil' Slugger's victims (at least from the first few episodes) appear in the opening. At one point, they appear in order.
Nando seems like your run-of-the-mill character of the day, but he ends up as a recurring rival for Ash and Dawn — competing in both the Grand Festival and the Sinnoh League.
The Sandile with sunglasses from the third episode of Best Wishes appeared again in episodes 12, 20 (where it evolves into Krokorok), and finally 64 when it's caught by Ash.
Look closely at the matchup screen showing the competitors at the start of the Sinnoh League — Tobias is on there. Additonally, Dawn is told of one of his matches- sespfically being told of his use of Darkrai- but she pays no heed to it.
An earlier example would be the fact that one episode occurring near the end of the Kanto arc involved Gary Oak fighting Mewtwo. The episode that followed has a scene with Mewtwo escaping from the Team Rocket headquarters, therefore setting the scene for Pokémon: The First Movie.
The earliest example would be from the very first episode: the Spearow that Ash threw a rock at comes back to terrorize local Pidgey and Pidgeotto in the season finale, having evolved into a Fearow (he can tell from the scar the rock left on it's face when it hit it). Also, Ash's Pidgeotto (the second Pokemon he catches) finally evolves, having spent exactly 78 episodes not doing so, and leaves his team to protect it's brethren from the Fearow. Doubles as Bookends for the first arc.
Nearly every minor character introduced early on becomes important to the plot later. The biggest example would be the little girl Red saves randomly in one chapter of the first Arc who later turns out to be Yellow, the main character of the second arc.
Similarly the Gold/Silver arc ends with Professor Oak confronting an offscreen child who wants to be a Pokémon trainer, in what is seemingly a throwaway homage to his opening monologues from the first Pokémon games. However, a few hundred chapters later in the Emerald arc, it's revealed that the nameless child was actually Emerald and that confrontation was part of his long journey towards becoming a Pokémon trainer.
There is a general rule about The Prince of Tennis: If you can remember their name, they will probably be back.
In Princess Tutu, the character Autor is always hanging around the library and later on in the background of scenes with Fakir. He later not only divulges an important plot point, but saves Fakir from a cult with a book.
Also Resha, who gets mentioned by Deerhound a little while before her massive significance to the story is revealed, and Saga Pendragon, who comes up as the one who made the prophecy about the 'two winds meeting' and later turns out to be the reason Resha faked her death to be able to aid the future.
Dana Sterling, the teen protagonist of Robotech's "The Masters" cycle, is one of these, as she first appears as a baby during the "Macross Saga" cycle.
In Sailor Moon, the episode that introduced Sailor Venus had her appear (in civilian form) in the background of a scene earlier in the episode. The camera also did a long pan on her and Artemis to make sure you didn't miss her. So it wasn't much of a surprise when she showed up later saving the Sailor Senshi. Of course it was more of a surprise in the DiC English dub, because they cut the long pan entirely and only the most eagle eyed of viewers could have spotted her before she got covered by a CGI Idiosyncratic Wipe.
A shot of her as Sailor V actually appeared in the first episode (cut from the DiC dub sadly) while Usagi and Naru are talking about her latest heroic deeds. She's referenced every so often from then on until she appears many episodes later in person briefly as a civilian and then Sailor Venus (wearing the Sailor V mask) as mentioned above
Much later, Setsuna/Sailor Pluto is introduced in a very similar manner to Minako. True, in her case Sailor Pluto had been introduced in the previous season, but her appearance on Earth was a surprise — unless you spotted her in the background.
DiC ended up making one of these while making a dub exclusive explanation shown at the start of Episode 1. If one looks closely, Haruka and Michiru/Sailors Uranus and Neptune can be seen.
On the Manga side, throughout Codename: Sailor V the other Sailor Senshi appear with minor background speaking roles, though not directly interacting with Minako. The Live action has a similar prequel known as Act Zero: Birth of Sailor V where they have minor background roles (Except Usagi who is saved by Sailor V).
Sands of Destruction features a fake World Destruction Committee who are using the fearsome reputation of and their (vague) resemblance to the actual members of the group to get free food in an early episode. Many, many episodes later, we see a wanted poster featuring those three instead of the real World Destruction Committee. Turns out, the Alligator Master mistakenly thought Taupy was a Bear instead of a Little Bear due to these posters, and so the robots will still obey him.
For the first few episodes of Servant × Service, a stuffed rabbit doll can be seen on the desk of Kenzou Momoi, the perpetually-absent office manager. During Episode 4, the characters (and audience) find out that the bunny is actually a robotic/virtual proxy that Kenzou uses to communicate from home.
Kanon is also introduced in a similar manner. Kenzou makes an offhanded reference to having a young daughter in Episode 5, and she subsequently joins the cast as a recurring character in Episode 6.
In Shakugan no Shana, a distinctive, heavily-burdened meido is occasionally shown trudging through exotic locales without any explanation; she eventually appears in the main setting and is introduced as an important character. In the movie, which is a remake of the first arc, she walks past the camera (and turns to look at it) in two news reports in the span of a day — once in the Gobi Desert and once on Mount Everest.
In an early chapter of the Soul Eater Baba Yaga arc, Kid and Maka notice the presence of two people following them. One of whom is a monkey, which both find funny. All we're told is that, though Shinigami told Medusa otherwise, the Shibusen group is being followed by Death Scythes and their meisters, although it appears to just be Azusa with her long-range communication/sniping skills. Chapter 59 sees Maka being saved from Medusa by the appearance of a monkey and a man in a bear suit, who turn out to be the South American Death Scythe Tezcatlipoca and his meister Enrique (the monkey).
Excalibur turns out to be this in the manga. At first he appears to just be a weird recurring joke—a weapon that for no apparent reason has a non-weapon form of a lizard-like creature instead of a human, which is powerful but has a terrible personality so no one can stand to work with him. Turns out he's one of the "Old Ones" that both the Big BadandBig Good belong to, as well as the Super Prototype all the human weapons are based on.
In the very first few minutes of Tengen Toppa Gurren Lagann, we not only see a post-timeskip version of Simon, we also see what appears to be Boota's human form. Inverted in that when the plot actually reaches that point in time, the events are very different from those depicted in the prologue. Rumour has it that the writers were making it up as they went along.
Tokyo Ghoul is very fond of these, with several seeming-minor characters later returning to play significant roles. Notable examples include:
Madam A, the owner of the Scrapper sent to kill Kaneki during the Dinner Show. Turns out, she is an associate of Dr. Kanou and handles matters for him. Kaneki's gang track her down and force her to lead them to Kanou's secret lab.
Souta, the Clown-masked member of the Ghoul Restaurant. He was the one that dropped the steel beams on Rize, triggering the events of the series.
Eto, the strange child-like member of Aogiri turns out to be the biggest one of the series. She is Yoshimura's daughter, the Half-Human Hybrid known as the One-Eyed Owl and the true leader of Aogiri. Not only that, her human identity is Sen Takatsuki, the author mentioned throughout the series.
The Clown Mask Gang, mentioned vaguely throughout the series as an old gang eliminated by CCG. In reality, they are pranksters that have been present the entire series and involved in several key events. Souta caused Kaneki's accident, and Uta and Itori have been "helpfully" guiding him along from one disaster to another with advice or requests, while Nico helped Aogiri capture Kaneki, and Roma spied on Anteiku for them. They promise to "have the last laugh", at the expense of pretty much everyone around them.
Ange Ushiromiya is very conspicuously name-dropped in the first arc of Umineko: When They Cry, but is not seen in that arc at all. She only starts to play a role in the third arc, and is in fact one of the most important characters (excluding Battler and Beatrice themselves) in the fourth arc.
Ange isn't the only one. In fact, Episode 1 contains references to every other Episode so far. Other notable character namedrops include Gaap and Goldsmith, which actually are pretty inconspicuous at the time.
The TIPS for Eiserne Jungfrau in Episode 5 mention the "SSVD" and its leader, "Wizard-Hunting Wright" or "Twenty Wedges". Guess who shows up in Episode 7, armed with S.S. Van Dine's 20 commandments?
In the first chapter of Until Death Do Us Part, a woman is pictured in one panel, with no explanation given for her. Five years of real-world time later, in a flashback arc about the main character's past, she is revealed to be, among other things, the last thing the main character saw with his actual eyes; her violent death, and the circumstances of it, were major factors in making him how he is now. Along with, y'know, blindness. See here.
In episode 22 of The Vision of Escaflowne a kindly beastman prevents a jaded young woman from eating a snail. Who are these two? The beastman is Jajuka, Dilandau's only surviving soldier under his command who protected him until he died saving his life, and the girl is Celena Schezar, Allen's sister who went missing...until it's revealed that Zaibach's sorcerers subjected her to fate alteration experiments and as a result of them, she turned into Dilandau Albatou.
An arc of The World God Only Knows consist of the protagonist looking for the remaining Chekhov's Gunmen, i.e. the girls that remember their capture.
Remember the little girl sitting next to little Emi when she first hears Kousei playing the piano in the flashback in early episode of Your Lie in April?. The final episode reveals she is a young Kaori. That means the meeting between Kousei and Kaori at the park in Episode 1 was not their first meeting, though Kousei didn't realize her appearence before.
The spirit of the Millennium Ring in Yu-Gi-Oh! is introduced as a recurring but ineffectual villain, usually defeated within a single episode in his appearances in the first two seasons, and he was apparently killed off for good at the end of Season Two. Some foreshadowing at the end of Season Three implies he got better, but otherwise he's never mentioned after Season Two. Then Season Five came — turns out he's the Big Bad of the entire series and was just waiting for his chance to strike.
In Yu-Gi-Oh! GX, Darkness (Nightshroud in the dub) takes a page from the spirit's book—introduced in the first season as the Superpowered Evil Side of Fubuki (Atticus in the dub), he's defeated and forgotten partway through Season One, save for a single episode where he came back in Season Two and was defeated again. Then in Season Four, it's revealed Darkness is actually an Eldritch Abomination that was just using Fubuki as a host, and he becomes the final Big Bad of the series. His host Fubuki is also a Chekhov M.I.A..
Enki of YuYu Hakusho appears as one of Raizen's old sparring buddies after the ruler's passing. He fades away until the reveal at the end that he won the Demon World Tournament, and is now king of the demons.