Alternative Character Interpretation: A ton, but particularly regarding Blue: strong independent woman with a judgmental streak, or cliche, hypocritical author avatar for psuedo-feminist speech?
The author has stated that Blue's judgmental attitude is an intentional flaw, so her hypocrisy in some areas (such as claiming to be a feminist while being dismissive of her cousin Orla) is likely deliberate.
Given that Gansey views Orla in a similar way Blue does, it could be a way of the author showing that Blue's Not So Above It All and is more similar to the Aglionby boys than she'd like to admit.
It's also worth mentioning that the diving contest, one of the most notable scenes of Blue and Orla disagreeing, is actually from Gansey's point of view. So, was the scene actually misogynistic, or was it evidence of Gansey's misogyny and Unreliable Narrator qualities?
Blue's relationship with Orla is also contentious, as some fans claim it's evidence of Blue's internalized misogyny while others claim it's The Glorious War of Sisterly Rivalry and not a representation of Blue's relationship with women in general.
Is Blue actually unfair to Orla, or are her feelings about her cousin justified given that Orla is something of a bully to her?
Adam in The Dream Thieves. Is he struggling with the anger and emotional backlash from an abusive father and taking on Cabeswater, or is he a selfish, misogynistic tool with anger issues that are never dealt with?
Significantly mitigated by Blue Lily, Lily Blue and The Raven King, where Adam gains control of his temper and shows much more respect for Blue. While he still has his detractors, his growth in those books has generally made fans more sympathetic towards his behavior in The Dream Thieves than they were when it was newly released.
Is The Gray Man largely another victim and just a weapon in Greenmantle's hands, or is he a willing murderer who's too easily forgiven by the narrative and the other characters?
Is Kavinsky unfairly vilified for his behavior, or was abusing Ronan and kidnapping Matthew enough of a Moral Event Horizon to justify his unsympathetic treatment by the narrative?
Draco in Leather Pants: Kavinsky's treatment of Ronan was explicitly written (and confirmed by Word of God) as an abusive relationship, including stalking, harassment, homophobic insults, manipulation, drugging him, violating his personal space, touching him without his consent, and kidnapping and trying to kill Matthew to punish Ronan for rejecting him. He also drugs his own mother without her knowledge, believes that "consent is overrated", and is the main villain of the second book. Nonetheless, he has a vocal fanbase who ignore, excuse, or outright romanticize his behavior. This is a controversial topic in the fandom, so let's leave it at that.
A case of Draco in Leather Pants, given the fact that he, among other things, kidnapped Ronan's brother Matthew as a way to attract his attention.
Tad Carruthers is a better example of this trope, given that he's had one scene in the entire series and still managed to garner a fanbase.
The "dream pack" (Kavinsky's friends Prokopenko, Skov, Swan, and Jiang) are probably the strongest example—half of them don't even have any lines, and in fact the only things The Dream Thieves actually says about them are their names, what cars they race Ronan in, and that Prokopenko was killed and replaced by a Living Dream. In spite of that, they're almost as popular as the main characters and have entire fanfictions solely dedicated to them.
Evil Is Sexy: Let's just say lot of readers became big fans of Kavinsky after The Dream Thieves.
Foe Yay: In spades with Ronan and Kavinsky. Not even spades, really. More like shovels.
Harsher in Hindsight: Call Down the Hawk reveals more about the scene in which Ronan dreamed a copy of himself as a decoy so he could get away from the crow monsters. Namely, it wasn't some mindless doll, he was a fully sentient perfect copy, meaning Ronan accidentally created a whole person as a meat shield.
While it was a funny exchange in the first place, fans love to point out how much better this exchange becomes after reading The Dream Thieves.
Gansey: From now on I need everyone to be straight with each other.
Ronan: I'm always straight.
Adam: Oh man, that's the biggest lie you've ever told.
Because of various hints, snippets, and some fanart shared by Stiefvater, the fanbase thought that at some point, Adam would turn into a tree. Come The Raven King and Blue is revealed to be half tir e' elintes, magic folk who can turn into trees.
Like You Would Really Do It: Strangely subverted with Gansey's second death. Before The Raven King came out, fans were convinced he'd die and stay dead. It wasn't helped by Maggie Stiefvaterconstantly teasing the fanbase. So at the end, the surprise came not from Gansey dying, but Cabeswater reviving him.
Memetic Mutation: Some of Gansey's more ridiculous passages about how much he admires Adam have led to "Gansey is obsessed with and overly impressed by Adam" becoming a meme among fans on Tumblr.
Gansey: adam i would die for you
Nightmare Fuel: Ronan's nightmares themselves. Especially when crow monsters start coming out and trying to kill him.
In Blue Lily, Lily Blue, Adam finding a bloody copy of Ronan's dead body.
Neeve being possessed while scrying under the beech tree in The Raven Boys. The whole thing is incredibly unsettling.
The Raven King pours this on thick. Eye Scream, demonic possession, reality warping, and gory murders are all in abundance.
One-Scene Wonder: Tad Carruthers appears for only a few paragraphs, in which he acts completely insensitive to Adam's disability and past abuse (coming up on his deaf side and cuffing his head), makes homophobic comments at Adam's expense, and in general acts like a complete ass. He's so hilariously obnoxious that he and the scene became a fan favorite.