An older book like Eberly's 3D Game Engine Design was more a loosely knit compendium of theory and algorithms. Eberly's more recent 3D Game Engine Architecture is closer to Gregory's in intent. Unfortunately, it's more a reflection of the idiosyncrasies of the author and his personal code base than an investigation of game engines as developed and used in the industry.
I've also heard good things about Mike McShaffry's Game Coding Complete. McShaffry is a game industry veteran, so he knows what he's talking about. However, it seems to be targeted at rank beginners, so a lot of the material might not be very useful to you.
Below that tier, of course, you have an endless array of how-to books written by incompetents. The worst is the "here's my shitty homebrewed codebase" variety.
For rendering in games, you'll need a separate book. Real-Time Rendering is the canonical reference. The first and second editions were my favorites. The third edition added a lot of information on recent techniques but at the expense of reading too much like an annotated bibliography, skating from topic to topic while rarely going into enough detail to be useful and often listing several alternative solutions to a given problem without comparing their relative merits and trade-offs. The first editions flowed more like textbooks and were thus better suited as introductions. Some of that might be hindsight bias on my part; I'm curious what others think who first learned the subject from the third edition.
I also want to give a shout-out to Christer Ericson's Real-Time Collision Detection book. It's full of clear explanations and practical, hard-earned knowledge that you can't get anywhere else. Plus, the accompanying code is robust and well written, a far cry from the usual crap that either straight-up doesn't work or is inextricably entangled with a massive code base (I'm looking at you, Eberly!).
