I agree on plot and coherence, but no atmosphere? I strongly disagree.
You're 100% correct, I misspoke and should have clarified. What I meant goes back to coherence - the atmosphere was just one of dread. Nothing specific to Quake. It was there, which made the game fun, but it wasn't distinct to Quake.
Part of it came from the darkness, part from the sound, and part from the emptiness. Quake was a very empty game, as were most from back then. You'd have eerie times of walking through a part of a level you cleared trying to figure out where to go next. No enemies to fight, as you'd killed them, but the knowledge that one may be around the next corner if you missed him the first time through, or in a closet (haha Doom 3), etc. It'd just be silence then (if I remember, which unfortunately was a step back from the distant roars of Pinkie in Doom.)
You don't get that with modern game design.