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.
Alternative Character Interpretation: Lord Asriel. Is he a callous would-be dictator? A misguided freedom fighter? An amoral ubermensch? An anti-hero? An anti-villain? Even Pullman sometimes seems to be at odds over this character.
Death of the Author: Interviews with Philip Pullman show that this is his view of how his books should be regarded ("I don't think it's the task of the author of a book to tell the reader what it means.")
Fridge Horror: It must be somewhat uncomfortable to have your inner nature projected for everyone to see, if not outright dangerous in some cases (eg the same-sex daemons = homosexuality theory)
Genius Bonus: Shortly after they meet, Will and Lyra question why "electricity" refers to what is called "anbarism" in Lyra's world, and why the stone called "electrum" in Lyra's world is called "amber" in Will's. Though neither child realizes the connection, the evolution of both terms alludes to the fact that the first observations of electricity (in our world, anyway!) came from pieces of amber imparting static charges to feathers and other small particles.
Holy Shit Quotient: In The Amber Spyglass we get a battle scene in another dimension between armies composed of, and this is all true: angels, witches, ghosts, cosmic horrors, interdimensional aliens, jet fighters, at least one Physical God as well as God himself, badass lilliputians, steampunk airships, soldiers armed with rifles, machine guns, flamethrowers and poison gas guns, monsters, animal spirits, floating fortresses, thunder and lightning, and, of course, armored polar bears.
Undermined - intentionally - by the fact that the battle is not really focused on, instead the story follows the two protagonists' brief appearance where they search for their daemons before killing God and hauling ass.
Shipping: There's Lyra/Roger, Lyra/Will, Lyra/Um...Lyra? Or Lyra/Pan. Absolutely mad, also includes Lyra/Scoresby, Lyra/Billy Costa, AND MORE! Seriously, next there will be a Shipping/HisDarkMaterials page.
Unfortunate Implications: While it's arguable if God Is Evil in this universe or if the Authority is just a God Guise, it remains to be noticed that this book seems to doom abrahamic religions as bad: all the characters somehow linked to Christianity (even some random priest met by Will at some point who wasn't even part of the antagonists) are portrayed as racist, superstitious, fanatic, intolerant Knight Templars who will doom evil anything the story classify as good. One of the witches even at some point delivers a speech where she states outright she considers any form of religion as bad. Oh, and the only time religion is mentioned in our world is to have a character mentioning she used to be a nun but left because she didn't feel it was good. Needless to say, the author had some problem because of this.
As a Reason.com review pointed out: Its kind of ironic that Phillip Pullman labels other works like Narnia as sexist and full of class snobbery, when Will the male hero, is the one who gets to fight the most and even becomes The Chosen One in control of the mystical Subtle Knife, meanwhile Lyra's greatest feats are accomplished by "feminine" wiles like lying and manipulation. The class snobbery manifests in that Lyra is the (illegitimate) daughter of aristocrats and is vastly superior in intellect and wits than her friends in Oxford (who also happen to be the children of servants) and Will being the son of a Royal Marines officer from the beginning.
There's also the fact that "all servants" supposedly have dog dæmons, suggesting that they were chosen as servants because of their dæmons; people who don't have dogs as dæmons can't get the job because they are considered too independent. It's not hard to think of racial profiling or job discrimination when it comes to this. Then again, Lyra's world is supposed to be heavily classist and unfair.
The hypocritical elements mentioned above may be lampshaded via the character of Lord Asriel, who is in many ways Philip Pullman's mouthpiece. He is passionate and sincerely dedicated to ending the tyranny and oppression of the Kingdom of Heaven. Other characters occasionally point out, though, that Asriel pals around with kings, continues to use his title, bullies and/or abandons his servants and has a good dose of contempt for the lower orders.