The X-Men AU fic The Wraith Saga features Jason Wyngarde being possessed by the Wraith (the Phoenix Force's Evil Counterpart) as a major plot point. The scene where the Wraith takes hold of him is a reference to the famous scene in Uncanny X-Men #101, when Jean first became the Phoenix.
Jean: Hear me, X-Men! No longer am I the woman you knew! I am fire! And life incarnate! Now and forever! I am Phoenix!
Jason: Hear me, mortals! No longer am I the man you once knew! I am the shadow! I am oblivion, and Death incarnate! Now and forever, I am The Wraith!
Winter War plays this trope for drama rather than humor. While Orihime is restoring Ichigo to control of his body, she makes a Call Back to something Ichigo said and did way back in the canonical Soul Society arc:
Orihime: Dont you remember what you told Kuchiki-kun — the person whos being saved doesnt get any say in the matter...
The Harry Potter/Justice League crossover Terminal Justice contains numerous references to Rorschach's Blot's stories Make a Wish, The Hunt for Harry Potter and Back in Black, in which Harry went around disguised as one "Mr. Black", in addition to several scenes from and references to Justice League episodes.
Notably featured are three uses of the Solar Flare attack to blind an enemy. In the first instance, Vegeta shouted it was like "walking in on Frieza in the shower"; the second victim several episodes later saw a brief image of a showering Frieza when hit with the attack. The third victim is Frieza himself, who sees a brief image of the second victim posing.
Back in the very first episode of Hellsing Ultimate Abridged, after Anderson cuts off Alucard's head only for the powerful vampire to reconstitute, Anderson demands to know how in the hell he managed to do that, to which Alucard responds, "Fuck you, that's how." In episode 7, this gets a magnificent callback when Seras goes full vampire after drinking Pip's blood, resulting in not only taking several levels in badass, but also regaining the use of the eyes that Zorin Blitz slashed out with her scythe. Zorin is flabbergasted, demanding to know how she is even able to look at her like this. Seras's response: "Fuck you, that's how."
TCotRWB's speech: "YOU'RE LUCKY I DON'T THROW YOU OUT ON YOUR FURRY BUTT ON THE SIDEWALK FOR THIS!" Thunderstorm's speech:"I SHOULD'VE KICKED YOU OUT ON YOUR SORRY FURRY BUTT YEARS AGO!""
Then there's a callback to earlier in the same episode - "Camping Trip Part 2" opens with a dream sequence where Calvin and Hobbes have resorted to eating tires. Later, the non-dream Calvin contemplates eating a tire.
Also, a scene in the very first episode has Calvin asking Hobbes "You Can Talk?", to which he responds, "Last time I checked." This sequence is repeated in its entirety four seasons later in "Invasion".
And if that does not work, remove the head, like I did to Grover in the epic battle the first chapter, and if you have not read that, go back and read it, or sleep you will go to hell! Beware of my warring!
There are entirely too many call backs in Concerned to even list. The best example is probably here when there are three separate call backs in the same day.
In chapter five of the Star Trek Online fic Bait and Switch the Galaxy-class starship USS Bajor suffers an attempted ramming attack by a Jem'Hadar attack ship. Captain Kanril Eleya flashes on "a horror story from before the Dominion War," the destruction of the USS Odyssey in DS9: "The Jem'Hadar". Then she blocks the ram by using the navigational deflector for its intended purpose: Deflecting incoming objects.
In The Legend of Total Drama Island, the Storyteller tends to lampshade her references to earlier plot points with the narrative flourish, "as has been told of before". When Lindsay is first revealed to be a gymnast, for example, the Storyteller describes in considerable detail Lindsay's achievements in that field. Many chapters later, when this secondary character trait becomes relevant again, the Storyteller says in pertinent part, "Lindsay was an accomplished gymnast, as has been told of before..."
In her narration, Courtney often references events from past seasons; she also does it sometimes when justifying her actions or giving advice.
Zoey invokes her 'Commando' personality in the boxing challenge, which makes her a much more effective, tougher fighter.
For How To Survive In Middle Earth When You're A Teenaged Girl, the "Doodles in the Margin" call back to the main story. In "Doodles" chapter 2, Elrohir calls back to the main story, book 1, chapter 14. From his own memory, Elrohir repeats his lesson to Priscilla. He says the same lines and makes the same motions. Priscilla says, "You remembered."
A Posse Ad Esse has two of these from the first chapter - Dr Spieler mentions two therapeutic setbacks since she started working in the stead of Dr Kindermann, one involving a hypodermic needle and the other involving Halo Stop Ultra. The first returns in Chapter 4 to aid Dr Wood's physical combat style; the other, in Chapter 14, the result of which the patients use as a springboard to restore Dub from his Angst Coma.
In an aversion of Hollywood Healing for characters and ship, Eleya and Gaarra are still on light duty after the events of Reality Is Fluid, and the Bajor's still having repairs done in the deflector room.
When briefing Eleya, Admiral Riker references the Terran Empire story arc in the "Cardassian Struggle" episode, as well as the revamped "Mirror Invasion" with the Terrans attacking Vauthil Station. He also refers to a Gul Antos, the subject of a Clear My Name plot in the diplomacy mission "Standoff".
Admiral Kree remarks that the Terran base and its defense sats will be a tough nut to crack. Brokosh asks if she wants them disabled or plain gone. This is about a year after he completely obliterated the main control center of Utopia Planitia Fleet Yards with a kinetic strike in Red Fire, Red Planet.
To From Bajor to the Black. Thrass gives Kanril Eleya the job of tutoring Tia and Sobaru in return for forgiving some of the bad grades she incurred after a messy breakup. Eleya's initially uncomfortable with the idea of tutoring Sobaru and Tia due to the campus rumor that they're a couple, since she's coming off of a nasty breakup with her boyfriend of a year, who was offered early graduation and a plum assignment on the USS Planck and left without saying goodbye. This after they were talking about getting married.
Eleya:(to Thrass) Youre putting me next to a blue-on-blue?* US Air Force Academy slang for a cadet romance. Also the slang for a friendly fire incident. Make of that what you will. After Dalton?
The Romulan Star Empire apparently fell into chaos (again) with the revelations that the Tal'Shiar were responsible for Hobus (missions "Revelation" and "Taris") and Empress Sela's kidnapping by the Iconians (mission "Cutting the Cord"). Velal, who succeeded Sela as Praetor after she crowned herself Empress, only recently restored order.
There's roundabout explanations of Velal's backstory as the Romulan general who turned up in a couple episodes of Star Trek: Deep Space Nine. Among other things the destruction of the Romulan flagship IRW D'ridthau at Cardassia is mentioned (the Aen'rhien, then an Imperial ship, apparently rescued the surviving crew).
Rear Admiral Taurik, the commandant of 40 Eridani A Starfleet Construction Yards, is the same Vulcan engineering officer who appeared in TNG: "Lower Decks" forty years earlier.
The fic references the launch of the Enterprise-B in Star Trek: Generations about halfway through, in the context of how stupid it was to launch the ship before it was fully finished. Eleya sarcastically asks Taurik if the remaining quantum torpedoes are going to be delivered Tuesday, and then tells him get her a full load by launch or she's not leaving port. Taurik thinks she's paranoid but she points out that over 350 people died in that incident because San Francisco Fleet Yards dragged its feet. When the inevitable happens, the ship is fully armed, and fully fueled thanks to Eleya bribing the shipyard's fueling manager with booze offscreen.
"Last Rights": Jhet'leya/Lyndsey Ballard from VOY: "Ashes to Ashes" is now the Kobali Armaments Minister, and adopts the Kobali created from Athezra Darrod.
The Stars Ascendant makes use of the images of the past which appear in the starry realm that Twilight Sparkle went to when she became an alicorn.
Strange Times Are Upon Us: The crew borrows Scotty's trick from Star Trek IV: The Voyage Home, capturing radiation from fissile materials, to repair their dilithium crystals so they can warp-slingshot around Sol to get back to the future. Rather than try to find nonexistent "nuclear wessels", however, they just mine and refine naturally occurring thorium offscreen.
Chapter 8 has Rika mention that Impersonator saying "baka!" makes more sense than M!Takeru saying "Onore!".
In Chapter 9, after Mika was called "Trini" while one of the heroes in Power Rangers Sword Dynasty watched Bioman, Rika makes references to how Trini received Mika's backstory only because of the former's actress' tragic death and the latter's on-screen death.
In The Fifth Act, Aeris jokingly refers to Cloud as a "nobody" after he calls himself one despite the Planet warning her about him when they first meet. She jokes that nobodies can't talk to the Planet. She starts to call him "Mr.Nobody" as an Affectionate Nickname. Later, Aeris uses it to remind Cloud that nobodies can't talk to the Planet. Which means the voice that Cloud is hearing is not the Planet, but Jenova.
During her second encounter against Kaito Kumon, the whole battle between Samus and Lord Baron harkens back to episode 46 of Kamen Rider Gaim, Kaito pins Samus down and is held sword point just like how he does to Kouta, but Samus stands up and equips the Athena Suitnote while in the aforementioned episode from Gaim Kouta is already in Kiwami Arms, during the climax of the battle, Samus emulates of how Kouta broke Lord Baron's sword and stabs him on the midsection with it. However, the fight ends with Deep Specter, Chaser Mach, Ryugen Melon Energy Arms, and Samus herself doing a four-way Rider Kick.
Cross threatens Zoro with Chopper's medicine in Alabasta, causing Zoro to remark "So many colors, and I couldn't cut any of them." Later in Skypiea, Zoro threatens Cross with the same, prompting Cross to mutter, "So many colors, and none of them would listen." Lampshaded by Soundbite of course.
When Sanji is informed that Princess Shirahoshi is underage and thus out of his range unless he wants to be a creep, he screams "CURSE YOU, FATHER TIME! CUUUURSE YOOOOUUUU!" Later, when Nami learns that a defeated Enel had flown off to the moon along with all her gold, she screams "CURSE YOU, ENERU! CUUUURSE YOOOOUUUU!" Bonus points for Soundbite responding with a deadpan "Seriously?"
Cross tells Nami that her facing down Crocodile directly would lead to her being eviscerated in 10 seconds (8 to monologue, 1 to laugh, and 1 for the eviscerating). Nami repeats this for what the sea will do to them if they try finding a Knock-Up Stream without the help of a South Bird.
When one of the Alabastan guards calls Cross and Soundbite scary for torturing the Unluckies with Vogon poetry, Cross responds with "Pi~ra~te." Later in the story, Robin responds with the exact same phrase when Cross calls her out for playing dirty.
During their trip to the Logan Animal Sanctuary, Firebrand asks OL about the offer of making her his Manhunter.
In the first episode, OL is afraid to use the Zeta Beam in fear of getting Telefragged. In Contingency, OL spoils Kid Flash's Hope Spot by pointing that the alien invaders' Zeta Beams cause Death by Telefragging.
In Dependency Day, OL comments how annoying how most copies of On Liberty only have the name of John Stuart Mill when it was co-written with his wife, Harriet Taylor. For Christmas, months later OL gives Diana a homemade copy with Harriet Taylor's name as a present.
In Ex Perdition A co-worker of Martian adult actor J'arrkn, mentions knowing Orange Lantern through his post Displaced interview with Cat Grant.
In Zatanna's introduction chapter, Artemis asks her why she can just say "Erif" when attacking someone. When Mistress Martian was attacking them, Zatanna does just that.
Paul jokingly tries to suggest that the Grecian Pantheon bring in gods or goddesses from other pantheons to make up for failing ones in their own to Diana, who laughs and says that they're not going to do that just so Paul can play "Musical Pantheons." Several months later, when visiting Themyscera, Paul accidentally causes Hera to divorce Zeus, causing a huge shakeup in the Grecian Pantheon.
Robb Returns: During his speech to the Lords and Ladies of the North in Castle Black, Ned mentions they need the men and the resources of the South, much like he did when he first talked with Catelyn about the incoming invasion of the Others. He also mentions that Robert's Durrandon blood sang true, like he did when he learned that Robert had found Stormbreaker.
After getting his Element, Wind Breaker regrets not getting the name of Applejack's brother, whom she'd been mistaken for. During Rex's meeting with Rarity, he asks for the name on Wind Breaker's behalf, but doesn't get it. The human Applejack finally gives him the name after he meets the human Big McIntosh in the flesh.
Chapter 39 is loaded with these, both to in-story events and to canon, including:
Vix-Lei mentions the time she talked about how she was looking forward to meeting any of Pinkie's relatives, since they'd probably be a real hoot. She then says, after meeting Maud Pie, that she was right.
Night Blade mentions Vix-Lei's crazy driving, and considers pony Rainbow Dash's flying to be even worse.
Page learns that Angel Bunny was real, and that he wasn't a demon, just a normal, bad-tempered rabbit... very similarly to Anon e Mouse Jr.'s first non-canon omake chapter, except for the fact that it's the Equestrian Fluttershy who explains it to her this time.
References are made to their time in Fluttershy's old cottage.
Night Blade and the human Rainbow Dash's previous visit to Elysium, when she slapped him repeatedly, is referenced.
The entire group's conversation references multiple past events, wherein the group learns the true identities of several of the Virtues' old "enemies", explaining the misunderstandings that came about in part because of Blueblood not understanding things quite right (as Rainbow Dash mentioned in chapter 31). The reveal on Trixie also references her human counterpart's scene at the vending machine.
Pony!Rarity makes a passing reference to her personal history with Blueblood, and later to the Diamond Dog incident in A Dog and Pony Show and the events of Sonic Rainboom.
The incident at the library from chapter 36 is mentioned, revealing that the three boys involved were the human counterparts of the Diamond Dog trio Fido, Spot and Rover.
The five older Bearers present reminisce on how they got their Cutie Marks, as they did in The Cutie Mark Chronicles.
Night Blade and Page both remember how they got their Talent Emblem/Cutie Mark, as mentioned in chapter 3 (for Page) and 28 (for Night Blade).
Page mentions the Magi of Stars being referred to as the patron saint of knowledge, something established in chapter 1 of the story.
Vix-Lei mentions her previous suspicions that Bulk Biceps was a minotaur in Equestria, along with what Pinkie told her about his actual Equestrian self.
In chapter 42, Page references the warning Balance gave her in her first meeting with the spirit.
Page's illusion sequence in chapter 45 is rather reminiscent of her introduction back in chapter 3.
Chapter 46 has Vix-Lei's rubber lizard make a second appearance, when she throws it at the Nightmare for a distraction.
In chapter 27, Rex seems happy at the idea of setting Vix-Lei on fire. In chapter 46, he actually does get to set her on fire, or at least her weapons.
The sequel, Picking Up the Pieces, continues the trend:
Wind Breaker has a run-in with Page's coworker Polished Apple, and gives her the message from Applejack about their ancestors not being happy about the way their family is doing things nowadays.
He also tells Page about his meeting with Diamond Back in the lead-up to the final battle, and Page recalls how Wind had saved her from the other griffon's carelessness.
Page's garden, where she and her fellow librarians grow their produce, is brought up for the first time since her first POV chapter in The Pieces Lie Where They Fell.
References are made to the events of the final battle with the Nightmare.
Chapter 5 contains brief references to Xvital's family background, which she previously told Wind Breaker about in the first story's chapter 13. Later, in chapter 9, Xvital herself tells Night Blade about some of it.
Chapter 9 contains further references to Xvital's past, as she explains to Night Blade about her poor experiences with nobility and how she'd inadvertently taken it out on him, something she'd realized (with Page's help) in story 1's chapter 30 and is finally apologizing for.
In the first omake chapter, Reel informs the Captains of the Bearers having met humans before, and some of the information they found out about Violet's ancestor during the Equestria Girls arc.
In chapter 15, Blazen Sun makes mention of the note Memorizing gave to Violet in chapter 2, leading to the reveal of its contents.
To canon - in chapter 9 of the sequel The Mare From the Moon, references are made to events from the episodes Dragonshy (Twilight mentions a dragons snoring and producing smoke that caused troubles), The Cutie Mark Chronicles (Twilight hatching Spike), The Return of Harmony two-parter (what Discord did the first time they met him), Secret of My Excess (Spikes Greed Growth-fueled rampage), Dragon Quest (their first meeting with Garble) and Gauntlet of Fire (how they first met Dragon Lord Ember).
At the end of the first story, Spliced learned that she was her worlds "banished pony", who would be trapped on the moon for a thousand years, and at the end of that time the stars would aid her escape. At the end of the second story, this proves true - Spliceds sentence ends exactly one thousand years after she was first sent to the moon, and she returns to Hesturland via the shuttle Aiding Stars, piloted by a pony named Escape Velocity.
In Double Agent Vader, the Rebellion's most highly placed mole in the Imperial hierarchy is a person code-named Ekkreth, with Leia Organa being one of the very few people who knows that Ekkreth is Darth Vader. At one of their meetings, Leia gets upset at the way Palpatine treats him, as if he were an inanimate possession instead of a person, and he agrees, "I'm a person, and my name is Ekkreth", echoing one of the first things he said in The Phantom Menace.