Affably Evil: Most villains. Even the demons are polite. That does not mean they're nice however.
Alice Allusion: Vorpal. Besides her Code Name, her friend Mr. Voice calls her Alice for lack of a real name to call her by.
All Girls Want Bad Boys: Subverted. One issue actually riffs on the idea in its name, but in the end, the girl decides that she likes the quiet guy.
All There in the Manual: Zig zags a bit. Reading only the main series is fine, and you get 99% of the stuff. However for all the small trivia about the future world, the prelates, faerie and everything else you need to not only read all the side stories, but the Q&A thread on the forums has stuff in it not answered anywhere. The RPG played on the forums (and set in the same universe) has some additional information too, but it's already more than 3,000 posts long.
Anti-Villain: Vorpal, clearly. Liedecker to a lesser degree.
Badass Normal: Liedecker manages to fight a freaking demon to a standstill. But the cake goes to George, who single handedly stops Rehenimaru's plan, and without any kind of weapon or battle training. Doubles as Badass Grandpa too.
The Bechdel Test: Lampshaded in one conversation that has been 100% about dating and boys, capped off with a character mentioning that she's probably going to fail the test she's studying for, administered by a Professor Bechdel.
Eagleland: Starts out looking like a Type 1 largely because the series is very US-centric until Volume 5. But Fridge Logic sets in when you realize that none of the core conflict would even exist without massive corruption and/or incompetence in the US government.
Enemy Civil War: Most apparent with the Brother Wright/Project TOME split, but Morganna/demons and demons/demon baboons, too. This seems to be a way of life in Faerie.
Enemy Mine: Even demons intent on hunting down and consuming the emotions of humans don't like Morganna.
Generation Xerox: Played with, a lot. Cyn and Warrick more or less are Alexis and Ian as kids, and thanks to stasis they even have the same roommate. In the "possible future" issue they even get their own super-group in the future. However it looks like they're not going to end up together, and the more Character Development there is, the more what looked like a Generation Xerox at first gets less and less xeroxy.
Word Of God says that originally, Cyn and Warrick were supposed to get together, but then the author ended up developing Tink, who was originally supposed to be a Romantic False Lead (along with Liz Von Stoker and presumably a few others who were then cut when Tink became a permanent fixture).
I Was Just Passing Through: Odd heroic sample with Hope 'helping' Vorpal with some smugglers when she just wanted to get to a transceiver.
Kid Sidekick: strangely enough, for all the gold and silver age feeling, deconstructed. The Whitecoat doesn't really want Damascus (Warrick's old prelate name) around, and finally has a chat with his parents to stop him after he accidentally slags key evidence. This leads them to enroll him at the Academy to train.
Even more deconstructed with Kay and Occult, since they're both kids.
Laser-Guided Karma: usually done in a positive way. All the people misguided or forced into villainy manage to get an happy end of one sort or another. It does help that most of the antagonists are overall positive characters.
Manic Pixie Dream Girl: Word of God describes Cynthia as this.
Mind Control: Both Avatar and Thunderhead's MOs. Morganna doesn't hesitate to apply it when needed.
Mutants: Called 'descendants' here. An interesting case in that while descendants are born with their powers, those powers are the result of experimentation during World War II, hence the name- because they are the descendants of the people experimented on.
Nightmare Fuel Station Attendant: Juniper has moments of this, casually commenting one things like how easily she could simply be shot and killed immediately after Cyn had a hallucination about all of her friends being killed horribly.
Orichalcum: The nearly indestructible metal orihalcite and its refined form, orihalcon.
The author has gone back and done a lot of editing, so at least it isn't a case of They Just Didn't Care.
Secret Identity: Played with. The Big Bad knew their identities from the start, their families mostly find out early on, but they still maintain their secret identities because of all the new enemies they've made.
Superpower Lottery: Some people control universal forces, some people... are prematurely bald.
Take That: The briefly seen villain Wartorn more or less *is* Mark Millar and paraphrases Millar as a justification of his villainy.
His real name is 'Mark Miller' in French.
Thou Shalt Not Kill: Constantly. It's rare to even have a villain kill someone. Not for lack of trying on their parts, though. Morganna seems to be immune to this rule.
Tome of Eldritch Lore: The 4, each of which contain the source code for the universe's local magical laws. All have their own force of will, are extremely dangerous, and perhaps most worryingly, can be photocopied or digitized with both copies retaining those attributes. One of them is called the Book Of Madness.
The Book of Passions in seems to think it's perfectly okay to sic monsters on its Chosen One.