Beauty Is Bad: While not every attractive character is evil, most of the evil characters are attractive (and immediately described so). Indigo herself is a subversion; she's stated several times to be fairly attractive, although not much focus is put on her looks.
Bittersweet Ending:Indigo's long-lost fiancé Fenran resurfaces. Indigo kills him. It's for the best. The endings of several specific books count as well. (For example, in Infanta, Luk Copperguild—aged thirteen—becomes the king of Khimiz after losing his father, his uncle, and the girl he's loved since childhood. And in Troika, Fenran's relatives are freed from a family curse, but not before it devastates them.)
Blessed with Suck/Cursed with Awesome: How Indigo's immortality and Grimya's speech and telepathy are treated at first. (Grimya's immortality, on the other hand, was a reward for being such a loyal friend, and is never treated otherwise.)
Blind Seer: Karim Silkfleet, in Infanta. Niahrin may partially count as well; she has the second sight in her bad left eye.
Lady Macbeth: Carlaze's scheming does a number on the Bray family. She and her husband get their just deserts in the end, but it's pyrrhic as hell.
Lolicon: Augon Hunnamek plans to marry Jessamin on her twelfth birthday. He later steps that up to her eleventh birthday. Of course, she turns out to be the avatar of the Serpent who Devours...but even so.
Meaningful Name: Indigo takes on that name because the color represents death and mourning in her homeland. The seeress Phereniq is instrumental to Augon Hunnamek's successes; her name is a derivative of Veronica (although she's decidedly not one) or Berenice, both of which mean "bringer of victory." Augon himself has a surname containing the word "human," which may foreshadow the fact that he is not, in fact, the demon in Infanta. The Brabazon family in Nocturne are all named after virtues...and while some of them live up to their names, the rather insufferable Modesty is a blatant subversion.
Red Herring: Infanta is the most blatant one. Indigo spends the entire book plotting to bring down Augon, thinking that he's the avatar of the Serpent who Devours. And then the real demon—Jessamin—ends up eating Augon.
Satellite Love Interest: Fenran (to Indigo) and Jessamin (to both Luk Copperguild and Augon Hunnamek). Or so you're led to think; both end up subverted with a vengeance, and not in a good way.
Star-Crossed Lovers: Indigo and Fenran, or so you spend most of the series thinking, anyway. Also, Moia and Gordo in Troika—until Carlaze interfered, with tragic results—and Yima and Tiam in Avatar (probably the only example in the series that ends well).