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.
Author Tract: Readers could be excused coming out of Codex thinking that Stross is an atheist, especially after the portion where Johnny reasons out to himself why Christianity is self-contradictory. However, the book both has a somewhat Unreliable Narrator in the form of Bob, and Bob has a Black Best Friend who's a vicar and good man, contrasted with the religious fanatic villains.
Of course, Stross isan atheist. But inferring such from his fiction seems both presumptuous, in that any even halfway decent fiction writer should be capable of writing characters whose beliefs differ from his own, and unnecessary, in that the author is perfectly happy on his blog to state outright that he believes in no god.
Also, it is an Author Tract - Bob's. It's a cross between his memoirs and a guide to hunting down cults hiding under other faiths. He lives in a universe where Christianity (and every other religion butone) is objectively untrue. That's kind of a required element of Cosmic Horror, for if there's a prophet-shaped escape hatch then the setting is no longer Cosmic Horror and becomes a differentkind ofAuthorTract. Bob is busy disabusing potential readers In-Universe of this particular hope that things aren't all that bad. (Also also, Johnny doesn't reason that Christianity itself is self-contradictory, so much as that the faith in general is highly schismatic, which has been true since theearliest days of the faith.)
Which doesn't quite justify how the story treats Americans.
The scene in Rhesus Chart in which the Scrum tries out their new powers as well as any time any of them drink blood in company. "Two Vampires with clipboards walk into a bar..."
Fridge Brilliance: The choice of codewords for various operations and assets seems incredibly stupid at times - when you put a code name on something, you want it to be completely non-indicative of the subject to avoid hinting what it's about. CASE NIGHTMARE GREEN is a bit dumb because "nightmare" suggests something very bad indeed - as does SCORPION STARE for a basilisk weapon, or MAGINOT BLUE STARS for an occult defense network made of same. It becomes brilliant again with the realization that these are Bob's memoirs, and like his own name, we're not getting the actual codewords - we're getting fake ones that are indicative of what they're talking about for reader convenience, so he can talk about them in the context of his memoirs without giving away the actual operational codewords of any asset or event.
Hilarious in Hindsight: A conversation between Bob and Mo in The Atrocity Archive reveals that In-Universe the reason volume four of Donald Knuth's The Art of Computer Programming hasn't been published yet is a Laundry gag order. ("He doesn't publish it, and we don't render him metabolically challenged.") In Real Life, the first part of volume four finally came out the year after Archive after spending nearly four decades in Development Hell.
Of course, the "Volume Four" which Knuth finally published may or may not bear even the slightest resemblance to the Volume Four which the Laundry placed on its Index Expurgatorius, and any such difference may or may not have something to do with the extreme length of the interval between Volume Four's publication and that of its predecessor. The real surprise here is that Knuth, a United States national, had the good fortune of having his publication schedule interdicted by the Laundry, instead of falling under the much harsher sway of the Black Chamber.
Paranoia Fuel: "The Concrete Jungle" runs on this for a good chunk. Any security camera on a WiFi network can be turned into an instant death ray if you walk into its line of sight. Have fun.
Perhaps even worse is the wide-field amnesia geas in "Equoid." Why does this part of Sussex seem relatively quiet and depopulated? Because the unicorns have been allowed to roam free, have eaten whoever they run into, and no one even notices the dead are missing.
Shallow Parody: The Jennifer Morgue didn't win many fans over with its attempt at Bond meets Lovecraft.