In White Night, a minor character from Storm Front comes back and plays a significant role in the plot. Additionally, an aspect of one character's Backstory which was mentioned only twice in the entire series (Once each in Storm Front and Death Masks) is expanded on, and becomes a major Plot Point.
Survivor's Quest and Outbound Flight, very different novels set 50 years apart, were written together, so there are calls between them. Survivor's Quest also has at least two Call Backs to the Original Trilogy. "I want to go with you", a young untrained Force-Sensitive who wants to help an older Jedi, and Dean Jinzler, brother of a Jedi, who'd been passing as an ambassador.
Jinzler: I'm not an ambassador, Guardian. I'm an electronics technician. Like my father before me.
Jedi Apprentice has Qui-Gon Jinn commenting to Yoda about not-yet-a-Padawan Obi-Wan Kenobi. He tells Yoda that the boy fought ferociously, which isn't a trait he likes to see. Yoda mildly says that this is like a boy he knew long ago. Qui-Gon assumes Yoda means his fallen apprentice Xanatos, but is told "Not speaking of that one. Of you I spoke."
Rebel Force, set many years ahead, has Obi-Wan as a Force Appartition describing Luke to Yoda, who says he's reminded of a boy he knew long ago. Obi-Wan immediately assumes he means Anakin and jumps to Luke's defense, saying he's nothing like that, but Yoda tells him he means Obi-Wan.
In Labyrinth of Evil, Anakin and Obi-Wan use the Linked List Clue Methodology to try and track down Darth Sidious. Many of the clues pointing toward Sidious were seen back in The Phantom Menace: Nute Gunray's mechno-chair, which provides the first break, is the same one he used on Naboo; Anakin and Obi-Wan find a pilot who delivered Darth Maul's ship to him from its manufacturer; and Sidious apparently uses a U-shaped speeder bike of the same design as Maul's to get around Coruscant quickly.
Two to Ben's previous visit to Tatooine during The Phantom Menace: he has a healthy fear of sandstorms, and knows something of the Tusken Raiders after an (offscreen) encounter with them during that film.
Most people call Annileen Calwell "Annie." Ben refuses to, both to maintain some distance and because it reminds him uncomfortably of Anakin.
Jabba's people are leaning on Orrin for payment because the new Galactic Empire is making business uncertain, so he wants cash on hand.
While never directly spelled out in the narrative, it's obvious that the event a few years earlier that spooked the Tusken Raiders and led to a decline in their fortunes, as well as those of Orrin when demand for the Settlers' Call dried up in turn, was Anakin's massacre of the Tusken tribe that killed his mother in Attack of the Clones.
In The Chronicles of Prydain first book The Book of Three Taran helps a gwythaint, one of the dark lord's creatures, against the advice of his more experienced companions. The gwythaint appears at the end of the final book The High King and buys Taran some time at the expense of its own life.
Dale Brown does this from time to time. For example, in Warrior Class, Dave Luger is angered and emotionally crippled when he meets one of the former personnel at the Soviet base he was rescued from in Night of the Hawk. In A Time for Patriots there are a few, such as the nanotransponders from Edge of Battle being used on the FBI agents and Pat being reminded of Hal Briggs's death.
Ma Gasket shows up in Son of Neptune wanting revenge on Jason, Leo, and Piper. Percy also shows up to reclaim his place as a main character after being absent for the first book.
"We've got a dam hole." And this one is from the original series.
When Percy shows up again after falling off a giant cliff and Hazel and Frank are surprised, he mentions that he's fallen from higher, which was another reference to the first series.
A lot of references to the past series show up in House of Hades, the curses from past enemies that Percy and Annabeth encounter in Tartarus and Percy's brief time on Ogygia being just a few.
Some of the centurions in Son of Neptune are caught playing Mythomagic, the same card game Nico was obsessed with in his first appearance. Later, when asked how he knows what a katobleps is, Nico admits it's because he remembers them from the game.
"Hey, Rache," Jenks said, dropping down from who knew where. "Your back is clear. And what is Plan B?" My eyebrows rose and I looked askance at him as he flew alongside, matching my pace exactly. "Grab the fish and run like hell"
Then, two books later, this exchange takes place...
"Plan B?" Ivy said. "What is plan B?" Jenks reddened. "Grab the fish and run like hell," he muttered, and I almost giggled.
From The Lord of the Rings: Tom Bombadil gives Merry, Pippin, and Sam a long knife (a sword to a Hobbit) taken from the Barrow-wights. The enchantments on these knives, or at least Merry's, play a MAJOR role in saving Minas Tirith.
In the third book of the Knight and Rogue Series Burke, while boasting about his pack of magic hounds, mentions they're immune to the drug Aquilas. Though it got no mention in the second book, it was discussed several times in the first before the characters actually drug somebody with it.
In Duck and the Diesel Engine, the big engines think Duck is making fun of them. While making their plan, they say "He did it to us, we'll do it to him, and see how he likes it" - and in the next scene they're blocking Duck line to the sheds, just as he and Percy did in Percy the Small Engine.
The BIONICLE books contain examples aplenty, due to their generally tight continuity and because certain characters, objects and plots had a tendency to go missing for many novels before suddenly resurfacing. One of the more famous ones is the fear displayed by Air-type characters to go left.
The Hercule Poirot novel Cat Amongst the Pigeons has a callback to Mrs McGinty's Dead, when Julia explains to Poirot that she thought of coming to him because her mother is a friend of Mrs Summerhayes, whom Poirot stayed with when he was in Broadhinny.
Done frequently among the numerous narratives in World War Z. A diver who specializes in underwater zombie combat mentions the Chinese sub that was sunk in an earlier story told by a Chinese submariner. Todd Wainio and his squadron come across the church that Sharon the feral child had been trapped in during the Great Panic. Wainio also serves with the girl who sang "Avalon" at the Battle of the Five Colleges. Arthur Sinclair still hopes to arrest Breckinridge Scott. Jurgen Warmbrunn mentions having come across both the psychological evaluation of Stanley MacDonald and the blog of Fernando Oliveira's nurse in his research. Collins mentions MacDonald trying to find his peace among the monasteries in Meteora when discussing war veterans trying to deal with their trauma from the war. It's also strongly hinted that the old man Kondo Tatsumi gets his katana from is the older brother of his master Sensei Ijiro. A photograph of the old man as a young officer shows he had a little brother that would have been about Ijiro's age.
The reveal that she was originally a pegasus makes sense, considering many of her more memorable moments have been in flight.
Her transformation into a Princess took her to the same hall of mirrors as Twilight it seems.
In Catching Fire, during the Quarter Quell, Peeta finds a pearl and shows it to Katniss, saying "If you put enough pressure on coal, it turns to pearls!", said by Effie Trinket in the previous book, to Finnick's confusion.
The Doctor and Cinder at one point help Karlax into a Zero room.
Halo: Hunters in the Dark sees the return of N'tho 'Sraom and Usze 'Taham, two Sangheili that serve under Thel 'Vadam (the Arbiter) and were last seen accompanying the player in Halo 3 (being the third and fourth players in co-op mode, respectively).
Wyndle grumbles that he was supposed to be assigned to a cobbler; a book earlier, the readers were briefly introduced to a Knight Radiant initiate who's a shoemaker. And it's probably a good thing Wyndle didn't get assigned to him, he was killed by the main antagonist in Edgedancer.
In one of the earlier books, Hoid mentions having once spent a better part of the year in the stomach of a greatshell; here, it's mentioned again, as it turns out Lift has witnessed the moment Hoid hopped into the creature's maw.
In the first The Spirit Thief book, Miranda is enraged upon finding a very Hollywood History book on wizards by one Mortimer Kant in a royal library. In the fourth book, Lelbon mentions offhandedly that "Mortimer Kant" is Illir's pen name, and the wind spirit publishes Hollywood History books to see if they can change the way people act.
In the second book of The Machineries of Empire, Mikodez mentions that he has learned all languages Jedao knew in life, including Tlen Gwa. That's in reference to short story Extracurricular Activities, where Jedao's attempts at speaking Tlen Gwa lead to quite a few more-or-less comical misunderstandings.
In Purgatorio Canto 27, Virgil mentions the time he and Dante flew the beast Geryon in Inferno to convince Dante that Virgil can guide through terrifying circumstances.
In Paradiso Canto 17, Dante references the many, many times he's heard people in Hell and Purgatory vaguely predict doom in his future when he asks his the soul of his great-great grandfather what that doom is.