All-New, All-Different Marvel: When Spider-Man, Iron Man, and Iron Spider (Mary Jane) fight the Regent, they note a strange sense of deja vu but feel that something important is missing. In Renew Your Vows, Alternate Universe versions of Peter and Mary Jane teamed up to defeat their version of the Regent with the help of their daughter, who doesn't exist in the mainstream continuity.
As noted under Book Ends above, the last panel of Laura and Gabby mirrors the last panel of her flashback with Logan in issue 1. In fact the presentation of the entire conversation between Laura and Gabby mirrors the one between Logan and Laura, right down to the position of characters in the panels. See here◊.
When Laura calls in S.H.I.E.L.D. to clean up her mess, she tells Maria Hill that while they detain Alchemax Genetics for her, and she, Gabby, and Bellona will hurt them a little to make them feel better. Again, this references the flashback with Logan in #1, where Logan tells her they won't kill the guy who almost blew her up with a bazooka, but they will hurt him a little so they feel better.
Squirrel Girl approaches Laura for help finding the "energetic-looking squirrel" she attached a tracker to in All-New Wolverine #3 after Mooney crashed his HUMVEE into its tree.
From the annual: When Gwen is in Laura's body and rambling about who she really is, Gabby immediately asks whether she suffered brain damage during the fall after plowing face-first into a car from several stories up. It's a reference to issues 1 and 6, where Laura's Healing Factor sometimes takes a moment to reset her brain after head trauma.
Issue 12: Laura tells Captain America she told Gabby she would never leave her while cradling her (supposedly) dead body, referencing her decision in issue 7 to allow her to stay.
Issue 18: Has a callback to the scene in issue 1, where Warren pats her on the head after she's been dumped across the street by a crashing Predator drone, because trying to hug her would just aggravate numerous burns and broken bones. After Kimura shoots Warren out of the sky in issue 18, Laura pulls him out of the water and does the same, with their dialogue reversed.
Issue 19: 16 issues after Gabby cheerfully tells Laura she should try using body armor, Laura finally integrates it into her costume.
Issue 21: Logan returns. Gabby mentions to Deadpool how he killed her, and is sort of like her grandpa, while Logan and Laura begin the process of mending the relationship after the events of Civil War II.
Issue 25: One of the takeout cartons on Laura's coffee table is marked "25 with chicken."
Quicksilver has to own up to his actions from House of M through to Mighty Avengers, where he stole the terrigenesis crystals, nearly killed some people and forcibly exposed Luna to the mists, started a war between the US and Attilan, and then blamed it all on Skrulls after Secret Invasion.
The Axis tie-in has Gambit think about his, Lorna and Sunfire's time as Apocalypse's Horsemen, back in Pete Milligan's X-Men run (with a sly acknowledgement of Horsman no. 4, Gazer, being C-List Fodder with Gambit not being entirely sure whether he died or not. Which he did.)
In Future Imperfect, a much older version of Rick Jones maintains a memorial room featuring the costumes, gadgets and weapons of the many heroes and villains who died in the nuclear holocaust that wiped out most of humanity. Here, a less aged version of the same character wears an outfit made up from parts of other heroes, including Ghost Rider's jacket, Doctor Strange's Eye of Agamotto and The Falcon's boots.
The 50s Avengers are based on an old issue of What If...? that explored a world where the Avengers were founded by 3-D Man and a bunch of obscure Atlas Comics (Marvel's predecessor) characters like Marvel Boy, Gorilla Man, Venus and the Human Robot. A canonical version of this team would later be introduced as the Agents of Atlas.
When Nyx's night falls, Bruce freaks at the thought he's still in Hell, having just got out from there in Immortal Hulk, and hulks out.
The Grandmaster's stealing Earth back in No Surrender is what's allowed the Queen of Night to break free from her imprisonment.
Hulk still holds a grudge against Clint for going along with Bruce's suicide plan in Civil War II.
Wanda's plan to fight Nyx has Monica form magical symbols using her powers, citing how Monica did the same fighting Shuma-Gorath back in Mighty Avengers.
Issue 2 has several scenes from the early days of the Avengers, only now with added Voyager. Her disappearance is explained as being the result of the Avengers' fight with the Squadron Sinister, from all the way back in Avengers issue 70.
The Challenger was exiled from the universe by the Grandmaster, only managing to get back in after "everything died".
Issue 10 begins with an extended prologue of Bruce Banner recounting the many, many ways he and the Hulk have died over the years.
Avengers vs. X-Men: When Cyclops gains the full power of the Phoenix, he utters the same phrase that was said when Jean Grey was first thought to be the Phoenix.
The 2009-2010 version of The Clone Saga had one that doubled as both a Mythology Gag of the 1990s saga that it's an Alternate Continuity story of, as well as this to The Night Gwen Stacy, as the 2009 story features Harry as the Big Bad, using cloning to bring Norman, who did die in this version, back — only for the clone to be a Morally Superior Copy who sided with Peter and Ben against Harry. When Harry tried the same "ram Peter Parker with spikes from the Goblin Glider" trick Norman died after he killed Gwen and when he revealed himself in the climax of the '90s Saga, Norman ends up Taking the Bullet instead, with the Mythology Gag being that was how Ben died in the original story — and the Call Back being, albeit in a different context from why it happened when Norman first tried it, the clone dying the same way the original Norman did.
Ultimate Comics: Spider-Man #1 (2011) opens with Norman Osborn observing an OZ-contaminated spider whilst telling a scientist the myth of Arachne, which happened in the opening panels of Ultimate Spider-Man #1. There's a bit of Fridge Brilliance in that the dialogue is just slightly altered to clarify a different moment in time, and that the spider, rather than the original 00, is marked 42.
Ultimate Origins features many scenes already seen in otherwise unrelated comic books, all of them with a Meta Origin that links them toguether.
Ultimate Galactus Trilogy: Reed mentioned the Fantastic Four adventure in the Negative Zone, where they met the alien Nihil. The knowledge they got there was cruxial for Reed to develop the weapon that was key to victory.
After the apparent death of ProfessorX, Cyclops throws in with his ex and a number of former teammates to keep mutants safe and teach them how to command their powers while maintaining tactical/philosophical opposition to the people running his old alma mater. The original concept of X-Factor (ca. 1985)? Or his post-Avengers vs. X-Men (ca. 2012) status quo?
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