Arch-Enemy: The Borg Queen with Janeway, Picard, and Seven of Nine.
Ascended to a Higher Plane of Existence: The possible fate of Janeway after what seems to be her death; Lady Q is a bit vague about it. We know it has bottomless cups of black coffee so it can't be that bad, right? Eventually it's more or less confirmed when Janeway returns in The Eternal Tide, a novel of the Star Trek: Voyager Relaunch.
The Atoner: Picard, for the destruction he wrought as Locutus. While he has come to terms with it since First Contact, it understandably still drives him.
Worf, for how his actions (saving Jadzia's life instead of the Cardassian spy Lasaran's) helped drag out the Dominion War when the information Lasaran had could probably have stopped it. As a result, he feels he doesn't deserve to be in a position of such authority as second-in-command of the Enterprise when Picard offers him the post.
Geordi in his attempts to protect Seven of Nine, due to his failure to save the female Borg Reannon (which is a Continuity Nod to the TNG novel Vendetta).
Awesome, but Impractical: It's pointed out in Greater Than the Sum that Borg Cubes are essentially this, hinting that there's more to the Collective than a simple desire for efficiency after all.
Blue and Orange Morality: The race known only as Them, who threaten to destroy the Universe because it's boring. And they're only stopped when Picard laughs at the absurdity of it.
Breather Episode: Q&A. And considering that it's about the end of the freaking Universe, that's really saying something about the other books, no?
Call Back: Pretty much every Borg-related plot thread in the Canon (and a few from the non-canon, like Vendetta) gets referenced, and many become key plot points.
Calling the Old Man Out: T’Ryssa in Losing the Peace, after her father finally makes contact, looking for information on her mother (specifically, if she survived the Borg invasion):
"Did you try to contact her after the Odyssey went boom? Did you try to find her any time during the entire Dominion War? No, this is about you. You had a near-death experience when the Borg hit Vulcan, and by some miracle, you lived. You managed to get rescued, fixed up, and flown to a hospital on the other side of the planet, where you got a lot of time to just lie there and think about how close you came to being just more sand piled on the Forge. Now you've got this big second chance, so now you want to reach out to all those you've hurt and make amends for all your wrongs".
Another New Frontier captain (actually TheCaptain of that franchise), Mac Calhoun, appears in Before Dishonor.
Cloud Cuckoo Lander: Lt. Stevens in Before Dishonor, though it turns out it was all an act, as he was actually Lady Q in disguise.
Cool Old Guy: Montgomery Scott qualifies as of Indistinguishable from Magic. He's a grandfather to his men in the Corps of Engineers, the Romulans know him simply as "The Miracle Worker", and the Klingon Empire is happy to loan him their top starship pilot because he asked nicely.
Evil Matriarch: The Borg Queen, naturally. (And in Before Dishonor, the Borg Queen is Admiral Janeway!)
Fantastic Racism: T'Lana has a bit of this towards everybody who isn't Vulcan, and Worf in particular.
Fictional Currency: The Ilec is a Karemma currency, evidently an alternative to the canonical Dirak.
Flanderization: Before Dishonor essentially flanderizes Worf, Seven of Nine, and Admiral Nechayev, presenting them in a surprisingly one-dimensional way, taking their various antisocial character traits (Worf's aggressive stoicism, Seven's cold precision, Nechayev's impatience and sharp tongue) and blowing them out of proportion.
Foreshadowing: The Borg Queen's threat to Lady Q that the Borg are analyzing her during their conversation, and that with time they will eventually be able to assimilate and learn the skills of the Q. This comes into play later in the climactic battle of Before Dishonor, see Ass Pull and Hope Spot.
Happiness in Slavery: Janeway experiences this briefly upon being assimilated, and the Borg Queen later tries to convince Seven of Nine that she will find this in the Collective. In fact, Geordi notes that Seven's willingness to meld with the Doomsday Machine as its pilot may be as a result of her subconsciously being more comfortable as part of the collective than as an individual being.
Heroic Sacrifice: Sara Nave in Resistance, narrowly avoided by Seven of Nine in Before Dishonor (but not by Janeway).
Hive Mind: The Borg, of course...especially the new Borg that give Starfleet an intense new war after they've "evolved" into consuming rather than assimilating. And yes, Pluto was one of the new Borg's first snacks.
Honor Before Reason: Admiral Jellico submits his resignation as Commander-in-Chief of Starfleet after the Borg Invasion, despite the fact that no one could possibly hold him responsible for the horrible losses suffered. When asked why, we are told that he felt his honor demanded it.
Hope Spot: Just when the Doomsday Machine is finally going to serve the Borg their ass on a silver platter once and for all, the Borg Queen teleports the Cube behind it (using the time/space warping skills she apparently gleaned from the Borg's analysis of Lady Q) and begins to absorb it, too.
Hurl It into the Sun: Starfleet Command briefly thinks that Janeway has somehow overcome the Borg Queen, recaptured control of her body and is attempting this with the Borg Cube when it veers off course toward the sun. They were wrong.
Jerk Ass: T'Lana, Lt. Leybenzon, Lady Q (though not quite as much as her husband).
Killed Off for Real: Most infamously Kathryn Janeway, though it's hinted that she may be able to return one day when, after Lady Q tells her she can't go back, she mentions how Spockgot better after the Genesis incident. The exact situation regarding Janeway's fate is revealed in The Eternal Tide, a novel of the Star Trek: Voyager Relaunch, which also subtly retcons some of Before Dishonor's events by exploiting the fact that when Q talk about Q, it's never entirely clear whether they mean Q, Q or even Q...
More recently, Scotty has also been killed, or so it seems. They Never Found the Body, so he might have made it...
Lampshade Hanging: In Indistinguishable From Magic, a character asks what the "NCC" in starship registries stands for. The character being asked - who is a starship captain, mind you - says he has no idea. This is pretty much the author acknowledging the fact that the frequently asked question has never been officially answered.
Living Ship: The defeated Borg cube from Resistance turns into one in Before Dishonor, making Janeway one of its first victims.
The Maiden Name Debate: In Greater Than The Sum, we have this exchange between newlyweds Jean-Luc and Beverly:
Picard: Good morning, Dr. Picard. Crusher: Good morning, Captain Crusher. Or would that be Howard? Picard: Either way, I'd be honored.
Never Found the Body: Scotty in Indistinguishable From Magic. He's probably dead, but for all we know he managed to transport somewhere safe in the nick of time. The other characters are all convinced he's gone, but we'll have to wait and see if he ever shows up again...
Nice Job Breaking It, Hero: Zelik Leybenzon's death scene during the Battle of Barolia, where he allows the Borg to assimilate Starfleet’s only major defence.
No-Holds-Barred Beatdown: The Borg to the Starfleet armada in Before Dishonor. It "made Wolf 359 look like a minor skirmish".
Noodle Incident: In homage to the original Noodle Incident, T'Ryssa Chen has the Tubegrub Incident.
Obstructive Bureaucrat: The Governors of Alpha Centauri and Pacifica in Losing the Peace, who at first don't grasp how desperate conditions are in the refugee camps, and spend most of their time causing further unrest and complicating the resettlement efforts.
Planet of Steves: Apparently all Voloczin (large creatures who look like an arachnid/crab hybrid) who leave their homeworld use that as their name. Thus we had a mercenary named Voloczin in Star Trek: Seven Deadly Sins, and another Voloczin who was the Challenger's Chief Engineer in Indistinguishable From Magic.
Pluto Is Expendable: Played devastatingly straight (although technically it's not destroyed, just absorbed; its matter is redistributed into the Borg Cube).
The Pollyanna: True to their pleasant, hospitality-based culture, the Risians are desperately trying to remain optimistic. Risa itself was destroyed in Star Trek: Destiny, a casualty of the Borg Invasion. The refugees are attempting to retain the expected "sunny Risian" outlook. Whether it will work out for them remains to be seen. One of the biggest problems is that Risa's natives pride themselves on declaring "all that is ours is yours". Now the Risians have nothing, and instead of hospitably receiving guests they are dependent on others for aid.
Relationship Upgrade: Jean-Luc Picard and Beverly Crusher in "Death in Winter", and Geordi LaForge and Leah Brahms in "Indistinguishable From Magic", though there's a bit of a Continuity Snarl with the latter in the ''Cold Equations'' novels. Since the events of Indistinguishable From Magic are referenced in other books leading into Cold Equations, this will likely be explained/resolved in the next series featuring the Enterprise crew, Star Trek: The Fall.
The Runaway: T'Ryssa ran away from home at age 7, after learning of the Vulcan kahs-wan survival rite that usually takes place at that time. She signed onto a freighter as ship's cook (the captain didn't particularly care that she was a young child) before being retrieved.
Sapient Ship: It turns out that Borg Cubes are (to a degree) sentient, and that the Borg and their new Queen have become a part of the giant one thought deactivated at the end of Resistance. Basically, the cube is a part of the collective too - in a sense, the Borg are the cube, not the drones.
Secret Test of Character: In Q and A, the beings known only as Them perform these on the inhabitants of entire universes.
Sheep In Wolf's Clothing: In Resistance, Picard attempts to infiltrate a Borg ship by partially reassimilating into the Collective as Locutus.
Shout-Out: The author of Greater Than The Sum mentions in the acknowledgements that the "Noh Angels" were directly inspired by the creations of Hayao Miyazaki and Chiaki Konaka (most likely No-Face from Spirited Away).
Smug Snake: Eborion in Death in Winter. He overestimated his ability to play the Romulan nobility off of each other, and was betrayed by his own aunt. So much for his ambitions to be proconsul – Tomalak gets that position instead.
Straw Vulcan: T'Lana. There's a damn good reason Picard wants her the hell off the Enterprise at the end of Before Dishonour. Even Spock completely washes his hands of her after she fails to hear reason. She does acknowledge her own faults in Greater Than the Sum, and herself admits she was completely out of line, as well as unprofessional in the extreme. Sadly, possibility for redemption was lost when she died in Star Trek: Destiny.
The Stoic: T'Lana, and then completely subverted after she departs, with T'Ryssa Chen.
Take That: Geordi and Seven discuss a character from the novel Vendetta, with Geordi commenting that the supposed Borg experts at the time of the earlier novel said there were no female drones, and Seven being understandably confused as to why that assumption existed. This is a reference to a disclaimer that was included in many copies of Vendetta regarding the plot surrounding that character, who one of the editors attempted to remove from the novel on the basis that 'the Borg are completely sexless.' (For the record, the novel was published in 1991, Seven of Nine was introduced in 1997.)
Think of the Children!: The Governor of Pacifica in Losing the Peace. He was concerned about refugees' effects on the Selkie breeding islands, but might possibly have been simply annoyed by the refugees. He insisted that the delicate environmental requirements of the Selkie young risked being disrupted by the settlers, and that in the name of the children steps should be taken to remove the outsiders. Most of the refugees had nowhere else to go, and really Pacifica should have been honoring its obligations to the wider Federation by accepting them. It was a complicated situation though - the governor might well have a valid point.
Title Drop: In Losing the Peace, when a character states her current fears about the rebuilding efforts in the aftermath of Star Trek: Destiny. She worries that the Federation might have won the war, only to risk losing the peace to their own complacency.
Trickster Mentor: Q, of course. He's been training Captain Picard over the course of most of their previous encounters, preparing him for an appearance before Them, the creators of the universe. Picard will represent all of creation before Them, and Q needs to ensure he makes a good show of it.
This actually punches I, Q out of Relaunch continuity, since in that novel it was Q who made a plea before the creator of the Universe.
Weapon of Mass Destruction: The Doomsday Machine from the Original Series; turns out it's a prototype anti-Borg superweapon., though admittedly, this was already theorized in Vendetta years ago, complete with an appearance by the completed, and highly pissed off and essentially sentient version, which has since flown into something approaching Warp 10, intending to go right for the Borg Homeworld and devour it.
What the Hell, Hero?: Geordi to Picard during Star Trek: Destiny, in response to Picard's order to construct a Thalaron weapon with which to wipe out the Borg en-masse. Geordi outright refuses to do it, whatever the consequences to his career. In fact, a fair bit of the Enterprise plot in Star Trek: Destiny involves Beverly calling this on Picard, too. Ezri finally gives him what for, as well.
You Cannot Grasp the True Form: Them, the creators of the universe (as well as several other realities), and the keepers of the meaning of life. Given that they exist outside the universe, it's not surprising they aren't described- no human could likely comprehend them.