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.
Also the fact that the book occasionally stops to preach about how masturbation ruins any chance at true happiness and love. Avi never masturbates, Lawrence discovers masturbation is meaningless after he's fallen in love, and Randy doesn't wind up finding true love until he's forcibly kept from masturbating for a few months. It makes you wonder if it's just a lengthy gag or an Author Tract on the subject.
Ho Yay — Alan Turing and Rudy. Or as Rudy put it, Alan would soon have an umlaut in him. Alan also propositioned Waterhouse, but was turned down politely.
Sci Fi Ghetto — The prologue to the Spanish translation makes it clear that "science fiction" also includes "fiction about science" (i.e. cryptography and information theory). The mass market paperback edition lists the book as "fiction" instead of "science fiction." Bookstores aren't convinced, however, and stock it in the "Science Fiction" section.
What's funny is that this forces them to stock the entire Baroque Cycle in the SF section, leading to considerable confusion.
Strawman Has a Point: G.E.B. Kivistik is basically a gag character, but once he's actually challenged on his statements, he stops being pretentious and points out that Internet access is a privilege not easily given to, say, the poor, and the advantages it can confer can leave large groups of society behind rapidly while granting enormous advantages to others, which depending on who you ask, has pretty much been what's happened in the ten years since the book was released. Even Stephenson, who is trying to load the deck, refers to Randy's defense as "an uncontrollable urge to be a prick."
Except for the part where he never actually explained himself, when challenged just used another metaphor, and then began trying to Ad Hominem Randy's arguments when he spoke up.
Randy doesn't really refute Kivistik's point either; he simply argues that his analogy is invalid because a network is not physically the same as a highway. Kivistik's 'ad hominem' attack, while smug, was in service of pointing out that Randy has lived all his life in a situation where advanced technology has always been available and can't really comprehend that the situation is different for others who have not had his advantages.
Cantrell's explanation of his feelings towards guns arguably counts.
The Woobie — Goto Dengo goes through arguably the worst the book can dish out. It helps that, unlike every other Japanese officer and soldier we meet in the book, he's not evil or holding the Idiot Ball.