Genius Bonus The discussion in one of the appendices of how magic works (by manipulating the "wave" that governs the probability of events) seems a fairly clear reference to/inspiration from quantum mechanics.
Magnificent Bastard: Sang-drax is one in Hand of Chaos when he first appears; he unfortunately comes off as more of a (literal) Smug Snake in the last two books. Kleitus is also one to a lesser extent, at least before he gets turned into an Ax-Crazy undead.
Moral Event Horizon: It's impossible to have any sympathy for Sinistrad after learning how he used and abused his teenaged wife Iridal and son Bane though Bane didn't exactly take it lying down...
Nightmare Fuel: In rough descending order of freakiness, the Lazar, the serpents, and the tytans.
Squick: The Haplo/Alake subplot in Serpent Mage. Not for the squeamish.
Tear Jerker: Bane's death, though you feel far more sorry for the mother forced to execute her own son than the psychopath-in-training who really had it coming.