I blame the Internet.
(If anyone cares, I've also reviewed the Penny Arcade coffee-table book and the fabled first collection.)
Webcomics don't necessarily age any quicker than any other artform, but videogames definitely age according to Moore's Law, and so any specific work that ties itself to that universe is going to quickly have its back catalog looking quaint. Penny Arcade Vol. 3: The Warsun Prophecies collects all of the Penny Arcade strips from 2002, which is so long ago one of my now-teenage sons was still in diapers. So this is a book about playing Metroid Prime and MechAssault and Warcraft III and Splinter Cell, along with a lot of other things that you and I (and, for that matter, probably Holkins and Krahulik) have forgotten about since then.
Warsun Prophecies was published in 2007 -- the Penny Arcade reprints have consistently run five years behind, for reasons unknown to me, and that may explain why they've never set the world on fire -- with then-current commentary from Krahulic explaining some of the jokes and references. (Including such often-necessary things as explaining what game they're talking about.) As far as I can tell, these annotations are not the same as the blog posts Holkins (and occasionally Krahulik) post on the website to explain current comics and other things going on -- they seem to have been new content for this book (as they were in the other volumes), separate explanations created five years after the cartoons.
In 2002, Krahulik's art style was still coalescing, and Holkins's references hadn't gotten quite as dense as they would later become: this is the early days, with the author-insert characters "Tycho" and "Gabe" looking cruder than they do today, and acting more like normal people. There's very little continuity in these strips -- they occasionally broke out a sequence later on, but hadn't really gotten to that point in 2002 -- so each one is, to use a modified version of Holkins's own explanation, mostly a three-panel JPEG posted Monday-Wednesday-Friday. Of such things was business empire made, if you can believe it.
This is early and fairly crude Penny Arcade, about games you mostly remember only vaguely. You could get the most recent book instead -- but that one only has the stories from 2008 in it, so you wouldn't be trading up very far. If you like Penny Arcade, grab any of 'em you can find: there's no sign that the reprints will ever speed up, so lateness will be your lot forever.
Book-A-Day 2014 Introduction and Index