Cryptonomicon/YMMV

Author Tract: To almost Ayn Randian levels in some places, but most notable when Enoch Root becomes his mouthpiece.
Non Sequitur Scene—Big Lipped Alligator Erotic Short Story.
- 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.
- Rudy and Bischoff, later in the book.
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.
Straw Man 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."
Tear Jerker -- Bobby Shaftoe's death.
- Cantrell's explanation of his feelings towards guns arguably counts.
Yellow Peril—Granted that Stephenson is fully backed up by the research in terms of the behavior of Japanese soldiers during World War II, but it is somewhat awkward to realize that Goto Dengo is the only Japanese character during the World War II sections of the book who is not, at best, holding the Idiot Ball and is not, at worst, an incredibly vile human being. Implying that their culture made them that way, while arguably somewhat true, really doesn't help matters.
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 a Complete Monster or holding the Idiot Ball.