The final season of Sailor Moon had oodles of references to the first season, mostly in the relationship between Sailor Moon and Sailor Star Fighter, including Usagi and Seiya meeting almost exactly like Usagi and Mamoru did, Seiya calling Usagi "odango" (what Mamoru called Usagi, more commonly known as "meatball head" to Americans), and culminating in Seiya throwing a rose to stop a bad guy while wearing an outfit remarkably similar to Tuxedo Mask's (with Tuxedo's theme playing in the background, even).
Berserk: There are frequent references to characters and events that happened earlier in the story's timeline, creating a sense of déjà vu.
During the part where Griffith rescues Charlotte from Ganishka, we see Borkoff, the Apostle who took Guts's arm.
Guts' fight with the Holy Iron Chain Knights in the woods is like a repeat of the Hundred Man Fight against Adon's mercenaries, with Farnese playing the part of Adon Coborlwitz and Azan playing the part of Samson. The part where Guts dodges several Mooks with spears attacking him is an almost exact reenactment. The main reason Guts loses this one is because he's completely messed up from his fight with Rosine.
The Lost Children chapter is focused around Rosine and includes her two insect henchmen, who were earlier introduced when they attacked Rickert's camp with the Count just before the Eclipse. Furthermore, Lost Children broadly follows the pattern of the Guardians of Desire run from volumes 2-3 using different characters in similar roles. Rosine takes the place of the Count and Jill takes the place of Theresia. Just like Guardians of Desire, it closely explores the backstory of one apostle and their Morality Pet as well as Guts' attempts to both pursue Revenge and scare away said Morality Pet with his act pretending to be a jerk.
Guts explicitly compares his confrontation with the reincarnated Griffith on the Hill of Swords to the time when they fought on a snowy hill to decide the issue of him leaving the Hawks. This time, he notes, he was the one who was defeated and deserted rather than the other way around. It also provides Guts with a rematch against Zodd, where he gets to show how much stronger he's become.
Guts' fight against Grunbeld slightly later is also much like Guts' first fight with Zodd, where he is facing a demonic Blood Knight who promises to destroy him if he does not put up a good fight. The way that he praises Guts after he succeeds in cutting his shoulder, and then transforms in a cloud of mist, is almost exactly the same.
The Majin Buu Saga of Dragon Ball Z is full of Call Backs to events all the way back to Dragon Ball, usually in the form of characters reminiscing about the old days. In one episode, nearly every single villain, no matter how minor, the main characters fought in Dragon Ball Z appears briefly in Hell, cheering on the current Big Bad... except Babidi, who's still angry that Buu killed him, and is rooting for Goku to give him what-for. Everyone except Raditz and Nappa. At least Nappa appears in a full scene in Dragon Ball GT and not some blink-and-you-miss-it cameo.
One Non-Serial Movie, Dragon Ball Z: Fusion Reborn, has a fairly humorous Call Back hanging a lampshade on the power-creep endemic to the series: as a result of Hell having a slight dead management problem, Freiza is alive and wreaking havoc again, and is dealt with (with one punch!) by post Buu-arc Gohan without even breaking a sweat.
In Dragon Ball Z: Battle of Gods, the Z-Fighters learn that they need six good-hearted Saiyans for Goku to achieve Super Saiyan God form, but they're one Saiyan short. Bulma mentions Vegeta's brother Tarble, who was introduced in a TV special three years earlier (but Vegeta dismisses the notion by pointing out that Tarble is on a distant planet and they have no way of contacting him).
Tower of God has a pretty sweet one: while being forced to kill her niece and rival/foe Anak, Androssi has a flashback to the training sessions with, where she had with Baam about loneliness and cafeteria food. Deciding get on over on Ren, that smug bastard, she instead kneels down to her and says "Anak, when this test is over, let's eat together."
Akane, climbing out of the outdoors bath, runs into Shinnosuke, a very forgetful boy. Like before with Ranma, Akane preserves her modesty with a towel, but the guy is completely naked. Notable in that Shinnosuke was, for a brief while, the only serious contender for Akane's heart.
While spending the night at a Chinese inn, Ranma is in the bath. Akane (really a villainous impersonator) walks into him; both of them look at each other in the exact same pose as during their very first meeting, right down to the towel.
There's a little joke in the first episode involving bulbs lighting up as each character realizes Haruhi is a girl, which didn't really make much sense until the reveal at the end. And then in the second to last episode Eclair suddenly has the same type of bulb pop up dark in her head, and then we see it light up when Haruhi interrupts her and Tamaki and walks out of the room again. Which almost doubles as a "Funny Aneurysm" Moment.
There's also a huge one to chapter 2 in the last chapter. Lampshaded a few times.
In Naruto, Sasuke, having received the Cursed Seal of Heaven, rises up after noticing his teammates in danger from the Sound ninjas, and declares, "I understand now. I am an avenger!" before showing then-uncharacteristic violence and ruthlessness against them. In Part II, Sasuke has gone into full-blown villainy, with other characters noting he has become colder than ever, even when compared to his state under the Cursed Seal. When Naruto is confronted by Tobi, and the latter tells him that even after having achieved his goal of killing Itachi, he is still focused on revenge by attacking the summit, Naruto refuses to believe it, to which Tobi replies: "Sasuke is a true avenger!"
Much like the above, Kabuto, once he reveals Dragon sage mode, starts using sound ninjutsu, a style which hadn't been brought up in several years and hundreds of chapters.
When the Byakugan is first introduced an off-handed comment from Kakashi implies there is a relationship between it and the Sharingan. This is never revisited until it is revealed that the ancestress of the Uchiha clan, Princess Kaguya, possessed the Byakugan.
In the first major arc of the series, Haku asked the then-rookie Naruto this question: "You said you wanted to become the best Ninja in your village and have everyone acknowledge you. Now, if someone who acknowledged you from the bottom of your heart appeared, wouldnt that someone become the most important person to you?" Now, in The Last: Naruto the Movie, Naruto has become a hero who has won the acknowledgement of the entire village, but he still hasn't found "that someone". The events of the movie help him realize that it's been Hinata all along, as she has acknowledged him from the very beginning, even if he never realized it before.
In Pokémon, Ash's Staravia evolves in a Pokéringer competition — the same way his Taillow evolved into Swellow. However, Staraptor has a far greater achievement. Unfortunately, James (who made it all the way into the finals in Hoenn) had a hold of the Idiot Ball that episode and gets eliminated in the first round.
Chapter 253 has multiple Call Backs to the reverse Wife Husbandry plan as several characters inwardly debate forming a Pactio, coming up against the age barrier around Kotarô and Negi and then remembering Asakura's plot.
Negima has a lot of Call Backs; seemingly irrelevant events can turn out to be much important later on, the most important of these comes almost 300 chapters in, when Zazie traps Negi in a Lotus-Eater Machine in which his parents are still alive and none of the events of the manga past chapter 15 had taken place. The entire thing is loaded with Call Backs to the very first chapter of the manga.
One particular call back in chapter 330 also serves as a Moment of Awesome: Evangeline grabs Secundum's arm to stop an attack on Negi and Fate while rising out of a shadow in the ground the exact same way she did when stopping Fate from attacking Negi back in chapter 51.
Negi's fight with Rakan is also a callback to his earlier fight with Takamichi, all the way down to Takamichi/Rakan showing Negi his new technique's weakness, which is the same in both cases (he telegraphs his movements).
At the end of the first episode of Code Geass, Lelouch's very first command with the Geass is for the Britannian Soldiers to die. At the end of the first episode of Code Geass R2, Lelouch's very first command with the Geass upon the return of his memories is the very same one.
Lelouch: Lelouch Vi Britannia commands you... All of you... Die! (the Britannian soldiers point their guns to themselves) Soldiers: Yes, your highness! (pull triggers)
The line in the little speech Lelouch gave accompanying that command in the first episode: "The only ones who should kill are those prepared to be killed." Near the end of the last episode of the second season, they flashed back to that. He meant it.
In chapter 249 of Hayate the Combat Butler, we learn that Santa, who appears in the very first chapter, is actually Nagi's Grandpa in disguise.
Despite the separate continuities across seasons, the Digimon dub pulls this off nicely. The 1st episode of Adventure is called "And So It Begins", and the last episode of Frontier features the line "And so it ends!" In terms of the franchise as an anime, it doesn't.
In the Throne arc of Kinnikuman, Meat finishes off an opponent with the Back Drop, specifically choosing it because it was a move Kinnikuman himself favored and struggled to master in the earliest parts of the series.
In Bakuman。, while the main characters are working with Hattori early on, Takagi mentions an idea he had of a story in which a boy tries to cheat on as many girls as he can as possible, and Hattori says it's a good example of a potential cult hit that most wouldn't be interested in, but a few might consider their favorite. In Chapter 113, while talking about what they should do next now that PCP will not get an anime and Mashiro's romance one-shot did poorly, the characters discuss the idea again.
Every incarnation of Fullmetal Alchemist adores Call Backs to a point that borders on fetishism. Expect everything that happens to be referenced in a later chapter/episode.
Classic example: when Winry confronts Scar for the first time, she learns that he was the one who murdered her parents. She's readyto shoot him, but Scar charges at her, yelling that if she can't shoot she should just leave. Ed dives in the way, shielding Winry with his body. Scar immediately flashes back to his brother defending him from Kimblee in the exact same way. The hesitation is enough for Alphonse to step in and kick his ass.
One standout example is when the last chapter contains a reference to Nina and Alexander's deaths, which happened over 100 chapters ago.
Chapter titles are often used to call back to related earlier events.
Chapter 459 calls all the way back to Chapter 1. Context: Ichigo has spent well over a year without his powers, eventually accepting an offer from Ginjou to try to get them back. This goes all kinds of wrong for various reasons, but as all hope seems lost, he gets stabbed by someone he can't see — meaning a Shinigami. Lo and behold, it's Rukia. And in nearly the exact same manner as he gained his powers in the very first chapter, Ichigo's back. The name of the first chapter is Death and Strawberry. The name of this one? Death and Strawberry 2.
"The Shooting Star Project" is used for chapters that relate to Shiba Kuukaku and her cannon.
"Rain" is a recurring theme that usually deals with painful memories. "Memories in the Rain" is the name of the chapter about Masaki's death and its effect on Ichigo. "Memories in the Rain 2" is about Kaien's death and its effect on Rukia. "And the Rain Left Off" is about both Ichigo and Rukia getting some resolution on their regrets. The "Everything but the Rain" mini-arc is about the traumatic events that tie Isshin, Ryuuken, Masaki, and Kisuke together.
"The Blade and Me" chapters involve Ichigo's relationship with Zangetsu.
When Hirako Shinji first introduces himself to the class, he writes his name on the board backwards and explains that he has a talent for reversing things. This is probably a reference to his shikai ability, which creates an illusion of an inverted world where left is right, up is down, and forward is back.
The first episode of Tengen Toppa Gurren Lagann has a full body shot of Kamina pointing upwards, followed by a closeup of his face and a closeup of his finger to the sides. The shot would be used several times in the series to indicate that something epic is going to happen.
The last chapter of the manga is a Book-Ends to the first chapter, from the chapter title to the surprise at the sudden game to fighting the weakest team in the league for the first game.
A minor one came in a full-color coverpage showing what all the characters were up to before the Hakushuu game. Agon is actually shown training, visibly struggling to do pushups while Yamabushi sits on his back. It's a call back to an earlier chapter where someone mentions his twin brother Unsui trains until he bleeds (while showing Unsui doing pushups one-handed with Yamabushi on his back) and Agon never had to work for anything.
In the earlier chapters while in Las Vegas, Monta killed his and Sena's amazing winning streak by betting everything on Red 21 which was the Deimon Devilbats' main color and Eyeshield 21's number respectively. Fast forward before the Japan/USA game where Yamato confronts Mr Don and bets on red. This time, the ball lands on Red 21.
For a series that starts out very Slice of Life, Popotan relies heavily on earlier events in its later episodes. Of particular importance is Mai's friendship with Konami (established in episode 2), which is not only called back to in episodes 9 and 12 (where Mai meets Konami's daughter and goes back to her time period, respectively), but also forms a crucial part of the anime's main theme.
The first chapter of Muhyo and Roji deals with the eponymous pair helping a girl whose friend had accidentally fallen in front of a subway train. In the last chapter, Roji waits for the subway, and the girl, talking with some of her other friends, recognizes him.
In Death Note, Light, dissatisfied with the state of the world, passes by some girls who are planning to go out to party and a young man who is angry about having to wait for his mother to pick him up. At the end of the manga, after Light has died and the world is going back to normal, Ide and Matsuda pass by the same types of people.
The dialogues in The Eccentric Family constantly alludes to earlier events that the audience has yet to be made a part of such as the Demon King Cedar incident, the Manpukumaru incident and the false Nyoigatake incident.
There are a bunch of things that happens in episode 11 that mirror things that happened in earlier episodes. They're mostly there to see how much Rikka has changed from the events of the previous episode, and how no one is really happy with the way things played out. The train station and drinks scene from episode 1, the convenience store food scene from episode 8 and the bridge lights scene from episode 9, as well as Yuuta putting away his chuuni related things from episode 1 are all mirrored to show how subdued Rikka has become without her delusions.
During Rikka's Stalker Without a Crush phase two years before the present story, she has seen the entire scene in episode 3 of Lite when Yuuta carried a rifle to escort Kuzuha.
In episode 4, when the monk mentioned his relationship with Haruka, there was a flashback from episode 1, when Haruka's mother brought the girl to him, asking him to exorcize Haruka.
In episode 6, Hiyori apologized to Haruka after recalling the former's bullying of the latter in episode 2.
In the penultimate episode of Nichijou, Mio and Yūko are confronted by the police officer Mio assaulted in episode 16 (a full nine episodes ago). The cop let's it slide after seeing that she had saved the life of a drowning child.
Little Busters! has an interesting example in that the opening sequence for the second season has heaps of callbacks to the original, both lyrical and visual. Firstly, the song begins with a line about how it's lonely to be by yourself and so 'we all gathered and joined our arms', taken directly from the first song, but then continues with 'but if we keep holding on so tight, we'll remain kids forever', referencing the main theme of this part of the story. We also have Riki running on a hill as before, except now he's alone and is running in terror rather than joy, and the 'scenery taking over the white space' effect from the original is reversed here. Finally, where in the original Riki and Kyousuke were walking towards each other and smiling in front of a blue sky background, here they stand in front of the same background facing away from one another, glaring. It all creates a pretty cool level of continuity.
In Gourmet Girl Graffiti, Ryou makes the daikon and yellowtail dish in episode 12 that she made back in the first episode. When she samples it, she notes that it's not very good despite the smell. But unlike the first time around (when she found the dish completely tasteless), she finally realizes it was sharing the food with someone else that made it taste as good as when her grandmother made it when Kirin eats it with her.
Heartwarming example of Your Lie in April: When Kousei reads the letter from late Kaori, she reminds him of various scene when they were together before.
Every ending of this show previewing the scene of next episode. The ending of OVA episode feature the scene from Episode 1 when Kousei first meeting with Kaori.
The very first chapter of Fairy Tail ends with Natsu and Happy running from the authorities, dragging Lucy along with them so that she can join Fairy Tail. Chapter 419 (set 8 years later in-universe) ends with the three running from the authorities again, this time to rebuild Fairy Tail.
My Hero Academia: Early on, the class holds a vote to determine the class representative. Midoriya wins with three votes, and Momo comes in second with two (everyone else having voted for themselves). Iida and Uraraka are subsequently revealed to have voted for Midoriya, but it's left unsaid who else voted for Momo. Eventually it's revealed far later down the line when Todoroki revealed that he voted for her. This revelation ended up giving her a much needed boost in self-confidence, as Todoroki is The Ace.
As in Thou Shalt Not Die, the Imperial Japanese Army temporarily takes over the Great Imperial Theater.
The final shot is of Sakura walking through the cherry blossoms at Ueno Park. This recalls the famous scene where Sakura does the same thing in the first Sakura Wars game.
City Hunter: Often plot elements of a previous storyline are mentioned in a following one. The best example comes is Kasumi Asou's second arc: an hypnotist had caused Ryo to become impotent to weaken him, and the first thing Ryo did was to use the antidote that had cured him from poison-induced impotence in a previous story arc.
The finals of Duelist Kingdom make several references to Shadi, and to Death-T.
Chapter 9 of the manga, where Kaiba and Duel Monsters first appear, is titled "The Cards with Teeth". Six volumes later, the chapter where Kaiba recovers from his Mind Crush-induced coma and duels Yugi once more is titled "The Cards Bare Their Teeth".
During Dark Bakura's battle against Dark Yugi on Kaiba's blimp, Yugi comments that he "never expected to play a game of cards with Dark Bakura." Dark Bakura replies with, "Heh, I had fun playing tabletop role-playing games with you," referencing their battle in the Monster World arc. During the Millennium World arc, Dark Bakura reveals that the Monster World gane was a warm-up for the Shadow RPG.
The Millennium World arc not only has several references to the Monster World RPG, but also has several references to Shadi's Shadow Games with Yugi at the very beginning of the series.
Vampire Knight: In chapter 65, when Zero is escorting Aidou to a cell, he apologizes for the linen not being lavender scented. This was a humorous nod to chapter 23, where Aidou upon bunking with Yuuki and Zero makes several demands that has Zero less than amused, one of them being lavender scented linen.
In the penultimate chapter, Zero attempts to talk Kaname out of sacrificing himself, explaining that what he does only brings pain to Yuuki rather than acting like compensation for his actions. This was possibly stemming from Zero's own self-destructive thinking throughout most of the story, not believing himself to be worthy of love and more deserving of dying, even before being turned into a vampire (for "stealing" part of Ichiru's life in the womb). Having eventually realized his self-loathing mindset had only served to hurt both Ichiru and Yuuki however, rather than being a said compensation, he recognized this similar kind of mindset in Kaname and thus confronted him about it, epitomizing his Character Development.
In Yamada-kun and the Seven Witches, when Yamada reads Sarushima's mind in chapter 107, she thinks "I want him to clean my room" - which is the thing she made him do when the two of them first met many chapters earlier.
All the way back in chapter 2, Nagisa's English journal entry mentions sushi is his and his father's favorite food, and in chapter 76 the two of them have breakfast together at a sushi bar.
In Chapter 51 / Season 1 Episode 15, Kayano reads a magazine on "Puddings of the World" instead of studying for finals. Her assassination attempt in Chapter 80 / Season 2 Episode 2 involves making a gigantic, explosive pudding.
The "weasel" which appears in the end of chapter 56 returns in chapter 88 to destroy the mini-tank of the boys.
Nagisa and Karma think back to the time they were nervous about flying in Koro-sensei's robe before their even more insane trip into space on an experimental rocket.
In the very first chapter, Nagisa attempts to kill Korosensei with a grenade at close range. Miss Azusa attempts the same thing in Extra Chapter 3.