After Mohg, the Pale King, and Duratek are all defeated in the fifth book, the Philosophers take center stage as the final villains in the sixth.
Big Bad Ensemble: Pretty much all the conflict in the series ties in to either Mohg or the Philosophers, who are working entirely independently of each other and indeed may be unaware of each other's existence. Mohg is the much bigger threat for most of the series, though.
Big Bad Wannabe: Several villains have ambitions that overreach their actual abilities:
The necromancer Dakarreth in The Keep of Fire schemes to use the stone Krondisar to become a god again and was The Chessmaster behind various events in the first two books and the backstory, but gets rather solidly defeated at the end of the novel without having come close to realizing his goals. Rubbing further salt in his wounds, it's later revealed that said Chessmastering was mostly Kelephon's work, and he simply manipulated Dakarreth into thinking it was his idea.
Kelephon himself plans big, serving the Pale King with the full intention of uniting the Stones himself and taking Berash's place as an Evil Overlord in pursuit of which goal, he was responsible for destroying Malachor and used Dakarreth as his catspaw. He actually succeeds in tricking Berash into giving him Gelthisar, only to immediately run into Melia and Falken and get rather unceremoniously killed off.
The Scirathi blood sorcerers in general. Billed as potentially worse than the Pale King if they get the power they seek, the serve as supporting villains in several novels, but their prideful belief in their own destiny to rule and severe case of tunnel-vision when it comes to their goals leave them open to being manipulated by other forces, such as Mohg and the Philosophers.
Bi the Way: Travis is attracted to both men and women at various points, and his bisexuality is never made a big deal of. He ultimately ends up with a man, Beltan.
Either/Or Prophecy: people are trying to save or kill Travis since he's fated to both save and destroy the world (usually based on how optimistic they are). Turns out he destroys the world then rebuilds it exactly the same only without the Big Bad.
Evil Overlord: The Pale King, a tyrant who dwells in his icy stronghold of Imbrifale and schemes to conquer the rest of Eldh.
Expy: A powerful but prideful wizard on the good guys' side becomes obsessed with certain powerful artifacts, which leads to his corruption to the Big Bad's side. He secretly plots against the Big Bad, hoping to gain control of said artifacts, knock him off his throne, and take his place, and commands his own forces that are allied to be distinct from the Big Bad's main armies. Though his treachery has some consequences, his plans fall through and he ends up dying an ignominious death at the hands of someone he'd wronged. Are we talking Kelephon, or Saruman?
Dark is Evil: Discussed and ultimate subverted. Mohg is the Lord of Nightfall and associated with darkness in general, but he was the god of darkness long before he separately became the God of Evil, and it's explicitly stated that darkness has a place in the natural order of things independent of Mohg's corruption.
Dragon with an Agenda: It's noted by several characters that Berash seems to care a lot more about conquering Eldh for himself than he does for freeing Mohg, though his actions serve his god's purposes either way.
The Fair Folk: Not as malevolent as the example, but not Disney either, and they have no compunction about manipulating the heroes to their own ends.
Wizards use Rune Magic, which relies on the idea that every object or concept has a particular rune, and to speak or write that rune lets you command it. There used to be three specialized kinds of wizards - Runebinders, Runespeakers, and Runebreakers - but only the Runespeakers still exist in the present of the story. A wizard who can do all three kinds of rune magic is called a Runelord, which Travis becomes. Wizards in the books are Always Male, though it's implied this is due more to cultural prejudice than actual restriction of ability.
Witches draw on the Weirding, an energy derived from living things, and can "weave" it to create various effects, which mostly involve Psychic Powers and influence over the natural world. Almost all witches are women; male witches exist, but are incredibly rare.
Sorcerers use Blood Magic to call up powerful spirits called morndari and bind them to perform tasks; the Scirathi further amplify their powers with special golden masks, with the caveat that they'll lose control of any bound spirits if the mask comes off. Whereas both witches and wizards require an innate gift, seemingly anyone can become a sorcerer if they're willing to pay the price, and while the former two kinds of magic-user are distrusted, sorcerers are outright reviled in most cultures which are aware of the practice.
Gay Cowboy: the minor characters Davis and Mitchell, two gay ranchers who have been together for over twenty five years.
Grim Up North: Imbrifale is the Pale King's domain, and it's the farthest north of the Dominions.
Has Two Daddies: Thanks to the powers of magic, this is a literal case! While on a ship, a Fair Folk trick Beltan and Vani into having sex with each other, both thinking that the other was Travis. Because of this, the child calls both of them her daddy, because they both played a role in her birth. Even if Travis didn't directly contribute.
Knight in Sour Armor: Durge is a mild example. It's not so much that he's cynical, he just expects the worse. All the time. But he is, rarely, capable of humor.
Load-Bearing Boss: Imbrifale as a kingdom has become entirely dependent on either the Pale King or Mohg for its survival. When both bite it at almost the exact same time, they drag every living thing in Imbrifale down with them.
Loads and Loads of Characters: Beyond the two main characters, the cast of major side characters balloons to about eight by the fourth book, and some minor characters that only show up for a few chapters get detailed backstories.
The Man Behind the Man: Mohg is the ultimate string-puller behind both the Pale King on Eldh and Duratek on Earth. Though his existence is implied from the first book with Brother Cy's cryptic warnings about "a shadow behind the shadow", and he is first named in the second, his actual role in the series isn't revealed until near the end of the third.
Mordor: Imbrifale is basically this, albeit arctic rather than volcanic.
Now or Never Kiss: Beltan kisses Travis (who he thinks has previously rejected him; in reality Travis has no idea he's even interested) while the former is mortally wounded. In an interesting twist, after Beltan recovers he apologizes, saying it was a coward's move and a terrible position to put Travis in.
Orcus on His Throne: Enforced; the Pale King has to work through the Raven Cult, the Necromancers, and Kelephon rather than doing things himself because he's magically bound to stay in Imbrifale. Once the wards come down, however, he personally leads his army through in no time.