- Acceptable Targets: Right-wing militia groups and their constituents. Any time they turn up, they're portrayed without any redeeming characteristics, harbor and enforce beliefs straight out of the Puritan era, and are usually trying to kill a lot of people for childishly petty reasons. So far, they've bombed an embassy in The Bone Collector, been annoying supporting antagonists in The Empty Chair (through Rich Culbeau's gang) and The Vanished Man, hired the Watchmaker to slaughter hundreds of soldiers and their families in The Cold Moon, and served as The Man Behind the Man for Billy Haven's mass poisoning scheme in The Skin Collector.
- Base-Breaking Character: The Watchmaker. Many readers love him for being Rhyme's Arch-Enemy and a brilliant Foil capable of matching his wits like no other, and for the labyrinthine schemes he inevitably draws up. Others hate him for his traits and Deaver's tendency to have him take the place of potentially more interesting villains, and think it's time for the novels to finish up his story for good and move on. Still others like him in moderation, but wish Deaver hadn't brought him out of jail so quickly after his arrest and made him into The Man Behind the Man in The Skin Collector.
- Early Installment Weirdness: The Bone Collector when compared to later installments of the series. Rhyme and Sachs can't stand each other, Fred Dellray is an Obstructive Bureaucrat presented as a minor antagonist, the killer's M.O. centers around races against time and is directly challenging Rhyme from the get-go, and not only does Rhyme never properly deduce the killer's identity — he focuses in on a wrong guess moments before the true Big Bad stabs his suspect in front of him — but he ends up taking out the killer himself by luring him in and biting his throat out, whereas later antagonists would always be shot or arrested in a sudden police ambush thanks to his deductions.
- Ensemble Dark Horse: Kathryn Dance, who received her own spinoff series, and lovable rookie cop Ron Pulaski.
- The Coffin Dancer ( both the real one and Red Herring Stephen Kall). Many wish the real Dancer would somehow return, given that he now has a personal reason to hate Rhyme and Sachs, and that he actively defied Rhyme's request to explain his backstory.
- Harsher in Hindsight: Much of The Broken Window with its focus on surveillance has become this in the years since it was first published, especially in light of the NSA's PRISM program, meaning that Deaver was actually pretty prophetic.
- The Kill Room deals in part with using drones to kill people, including US citizens, while abroad.
- Jerkass Woobie: Lincoln Rhyme to an extent, overlapping with Wheelchair Woobie.
- To a more murderous degree, Vernon Griffith / The People's Guardian in The Steel Kiss also counts. He and his brother were both mercilessly bullied in their school years, the latter to the point of suicide. His attempts to make friends and find love are consistently unsuccessful, and when he finally meets a partner with whom he feels a genuine connection, it's a woman (Alicia Morgan) who's openly only staying with him to seduce him into being her puppet for a revenge scheme, which results in him being forced to murder ever more people rather than trying to control his rage. In the end, he gives himself up to the police without resisting, and almost breaks down after learning that Alicia had planned to kill him when he was done with her plan. By the end, even Rhyme acknowledges that he's among the most complex and sympathetic killers he's ever matched wits with.
- Nightmare Fuel: Some of the more gruesome deaths depicted in the series, including:
- Being cooked alive under a steam pipe, cut open multiple times and left to be devoured by a Swarm of Rats, and having your flesh rendered off with a lye bath (The Bone Collector).
- Being stung to death by bees and being poisoned with insecticide in your car (The Empty Chair).
- Being bisected with a saw (The Vanished Man).
- Having your throat slowly crushed by an iron bar you've been forced to hold up (The Cold Moon). Although this one was staged with a stolen corpse by the Watchmaker.
- Every single death by electricity in The Burning Wire, from a makeshift Lightning Gun blowing up a bus station pole and riddling an unfortunate victim with the self-cauterizing metal pellets, to a whole hotel lobby getting fried out of nowhere.
- Being immobilized and skinned alive with a kitchen knife (The Kill Room).
- Getting tattooed with poisonous ink and left to die in protracted agony (The Skin Collector).
- Falling into an escalator's motor and being crushed to the point of almost splitting in half (The Steel Kiss).
- They Wasted a Perfectly Good Plot / They Wasted a Perfectly Good Character: The Skin Collector sets up a distinct tie-in to the plot and central antagonist of The Bone Collector, Lincoln Rhyme's debut novel and one of Jeffery Deaver's highest-regarded books, right down to the conceit of a masked man stalking the darker areas of New York and killing people in heinous ways related to an obsession with an element of human anatomy. Many fans were therefore displeased when the real component of The Bone Collector that tied into this plot turned out to be the Right-Wing Militia Fanatic organization, with Billy Haven being little more than a psychotic henchman and his obsessions reflecting his petty prejudices rather than the Bone Collector's tragic revenge scheme. The Bone Collector himself, Colin Stanton, is given a few cursory mentions (never by his true name, despite the Big Bad Duumvirate sharing the name Stanton) and otherwise treated like an afterthought in the grand scheme — Rhyme and Sachs don't even experience a touch of angst over the traumatic case being brought back up. And to top it all off, the whole charade was enabled by the Watchmaker, who was Faking the Dead. Some view it as a well-done series of twists that keep the book from feeling like a retread of earlier material, while others see it as Deaver going overboard with his reliance on faking the reader out and wish there had been a genuine reflection on Rhyme's first and most nostalgic case.
- The Woobie: Amelia Sachs. Her idolized father died when she was young, after which her mother became abusive towards her. She also has problems with self-destructive behavior and arthritis.
- Garett Haldon from The Empty Chair definitely qualifies. His parents were killed because they got involved in a pesticide conspiracy. Their murder also caused him to draw in some of the pesticide himself, making him lose his grip on reality and become a harsh Cloudcuckoolander. He was then placed under the care of foster parents, who are implied to have hit him on occasion, and was also pitted as a scapegoat for several murders involving the same conspiracy.
YMMV / Lincoln Rhyme