Charles Petzold and Jeff Atwood have gotten in a bit of a kerfluffle that, I think, is an unfortunate example of how online writing can escalate and over-dramatize disagreements between even two talented writers. I'm sure that Atwood appreciates Petzold's work and I'm sure that Petzold appreciates constructive criticism. I'm not going to link to the original posts, because I think that they were both perhaps overly curt and I don't want to fan any flames.
But I do feel strongly enough about the issue to say this: Petzold's Applications = Code + Markup is a very good book. It's dense in a good way (if you've been following the dustup, read the pages in Atwood's original post).
Petzold's work also has a conscious narrative philosophy. Petzold talked about this when he was writing the book. Atwood praises the layout choices made in another book (which I haven't read) and his arguments are credible. But Petzold, too, made deliberate choices on these very issues and I don't think that it's fair to dismiss those choices as if they were accidents of an outdated approach to book design.