Batman: Alfred made disparaging comments about Tim's ability to fold clothes the day he became Robin in Robin Vol 1 (1991). When Dick comes to Gotham to take over for Bruce as Batman during Knightfall (1993) he finds Tim's inability to do any household chores amusing and forces Tim to learn how to properly fold things since he's the adult in charge as Tim's father, Bruce and Alfred are all out of Gotham.
DC Comics Bombshells: Diana discusses constellations with Steve Trevor when she helps him escape from Themyscira. After the Battle of London, she and Steve comfort Supergirl after Stargirl's sacrifice, by saying that there will be a new constellation in her honour.
In Death of the Family, Joker tells Damian how he can't really get people to laugh without giving them a pharmaceutical push first. In fact, Batman was apparently the only person he could get to actually laugh. In case you're wondering, Joker is referring to The Killing Joke, or its ending. In addition, the Joker commits many crimes similar to the ones he committed in his first appearances back in the 40s.
The first scene of Green Lantern: Rebirth (which tells the story of Hal Jordan's resurrection and his taking up the Lantern mantle once more) is a call-back to Hal's origin story in the very first issue of the series. It starts with an Oan spaceship crashlanding outside of an Air Force base in the desert with an injured Green Lantern in the cockpit. But this time, the injured Green Lantern is Kyle Rayner.
During Dwayne MacDuffie's run on Justice League of America, Animal Man finally accepts that he's being mucked about by a villian who can control stories when he suddenly realises he's eating chicken. A subtle nod to the end of Grant Morrison's run on Animal Man, when Morrison's Author Avatar used the example of Buddy suddenly not being vegetarian to illustrate the power the writers had over him.
Grant Morrison's map of the Multiverse includes Wonderworld, a dimension that was featured in their JLA run. News articles have also mentioned that some of his characters from Animal Man would appear on one Earth.
They revisits some concepts they introduced in Final Crisis, such as President Superman and Earth-23, and Overman and Earth-10, and some they introduced in Action Comics, like the mention of Superdoomsday, and Optiman's allies Red Racer and Flashlight.
Earth-10's Batman is called Leatherwing, which was also the name of a pirate version of Batman (who according to The Multiversity Guidebook #1 is the Batman of Earth-31).
The variant cover to Society of Super-Heroes: Conquerors of the Counter-World #1 featured the Batman-esque version of John Constantine called Hellblazer. Morrison created this version in an issue of Doom Patrol, in a dreamworld that had more superheroic versions of the Vertigo-related characters. This world was seen again in the third The Books of Magic annual.
Sasha Norman, a.k.a. Sister Miracle of Earth-16 in The Just #1, was first seen in Seven Soldiers while Shilo Norman was forced to endure alternate lives in the Omega Sanction.
Countdown to Final Crisis gets a mention during The Multiversity Guidebook #1, specifically Superboy-Prime destroying Earth-15.
Morrison references it again in Mastermen #1. In Overman's dream of Lord Broken, the bodies at his feet are those of the Justice League Axis, the version of Earth-10's Justice League that Monarch recruited in Countdown to Adventure.
Mastermen #1:
Overman's wife mentions that his cousin, Overgirl, was just a clone created from his stem cells, and if he wanted he could have her replaced. It's said that the original Overman in Animal Man had his stem cells harvested by the government to create other heroes, his world's Justice League.
Overgirl's death "on a distant world" is another Final Crisis reference, and the scene of Overman holding her corpse is a reference to Supergirl's death in Crisis on Infinite Earths.
The Multiversity #2:
The corrupted Nix Uotan threatens to unleash his final attack after completing a rubik's cube in seventeen moves (something that's supposed to be impossible), much like how he regained his powers back in Final Crisis.
Red Racer and an army of alternate Flashes all use the "infinite mass punch" that Wally West used in Grant Morrison's very first story arc of JLA. He even comments that it came from "one of [his] favorite JLA stories."
The Empty Hand mentions that the Gentry is still feeding off the carcass of Multiverse-2, which seems to be the pre-Flashpoint Multiverse created after Infinite Crisis. This seems to highlight the discrepancies between the Multiverse as it is seen here, compared to how it was in Final Crisis.
Nix Uotan is seen with a monkey sidekick, possibly the typewriting monkey from Morrison's Animal Man and/or the monkey that helped Nix restore his Monitor powers in Final Crisis.
In Bizarrogirl, Supergirl watches a recording of the events of "Escape From Bizarro World" in order to find some clue to stop an enemy from eating the whole planet.
Swamp Thing Vol. 2 #43, "Windfall": Sandy's good trip is a general Call Back to Abby's in Rite of Spring. The Call Backs within Milo's bad trip are more specific, referencing the Swamp Thing's origin story (Volume 1 Issue 1 and elsewhere), the Patchwork Man (Vol. 1 #3), the Conclave robots (Vol 1. # 6), General Sunderland (Vol. 2 #6-21), the Rosewood "Mother" vampire, the Monkey King, a werewolf (Vol. 1 #4), the Un-Man Cranius (Vol. 1 #10), an alien (Vol. 1 #9), and finally, as the driver who accidentally kills Milo, Arcane.
In Wonder Woman (2006) Etta makes a comment about Diana's new side job being a huge improvement to slinging tacos, despite Diana's inability to lie being a hurdle in the spy business, as a reference to her previous job at Taco Whiz in Wonder Woman (1987).
With Wonder Woman (Rebirth) bringing quite a few Pre-Flashpoint Wonder Woman elements back into continuity this was inevitable as Diana sorts out which of her memories are true and false in the Post-Convergence 'verse. When Diana shatters the mirror she's talking to after she discovers her memory's been tampered with, the various shards contain callbacks to famous moments from her history. Some moments being:
Beheading Medusa from Rucka's first run in the mid-2000s
The Gorilla Knights and Diana defending her mother from the Circle from Gail Simone's run.
Wonder Woman: Black and Gold: When dealing with an invading First Born in "A God With No Name", Diana obstructs her vision with a piece of cloth - a reference to her famous fight with Medusa from Greg Rucka's first run.
