Certainly id's code is clean and well-structured, however I always had a tough time trying to grok it as a layperson. Comments (those within the functions) are relatively sparse, and the code often contains quite cryptic expressions that are somewhat bewildering to those without an high understanding of 3D graphics.

This, of course, makes perfect sense as an output from an industry leader in the field (Carmack). However it definitely requires a lot of foreknowledge and, dare I say it, a mathematical bent to follow with confidence.