These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Religious fundamentalists and cults are bad. However, while most of the religious people in the books are freaking insane, Valkyrie's family is Christian and a big deal isn't made out of it.
There are some Randian/Objectivist themes, though they're somewhat more subtle.
Landy obviously thinks that the relationship between Bella and Edward in Twilight is dangerous and unhealthy and viciously satirises it.
Complete Monster: Quite a few. There's Nefarian Serpine, Baron Vengeous, Dreylan Scarab, Dusk, Mevolent and Davina Marr. The Faceless Ones make them all look like pretty nice guys.
Crazy Awesome: Skulduggery refuses to give an answer on whether or not he is insane. Making that decision, he says, is the job of a psychiatrist. He is not a psychiatrist; he just punches people.
Die for Our Ship: Fletcher is considered by some Valduggery shippers to be either a complete moron or evil incarnate. Caelan on the other hand, is mercilessly mocked by just about everyone. Including the author.
Ensemble Darkhorse: Almost every single non-main character counts, although Ghastly and Sanguine seem to be the most popular.
China Sorrows is a prime example of this trope. And in heels too!
She gets outplayed by Eliza Scorn in book six.
Nefarian Serpine.
Narm Charm: A chunk of the series has some of this starting out due to rampant Awesome McCoolname syndrome, though justified because everyone chooses their own name. The names "Valkyrie Cain" and "China Sorrows" sound more like Dick Tracy characters, but they make it badass. And the name Lord Vile sounds really Narm-y... Then you get to the end of Mortal Coil and you see Skulduggery break down at the sight of him.
Remnant Tanith and Billy-Ray Sanguine kissing. Valkyrie certainly seems to think so.
Even moreso when you think about it. Sanguine had a very creepy thing for Tanith for a while. Now, he's got an evil, possessed, fully consenting Tanith. God help the poor thing if/when she comes out of this stupor.
On a somewhat more light hearted note, Valkyrie flirts with a guy at the Requiem Ball. What she doesn't realise is that she has his drunk father's vomit in her hair.
Lord Vile sticking his thumb in Darquesse's eye.
The end of Death Bringer has Valkyrie biting that... thing to get it off her while they try to get away from Lord Vile. Even Melancholia stops being mean to her for a moment.
What Do You Mean, It's for Kids?: This series is advertised for children 9 and up. This would utterly shock the people who have read the series without knowing this.