Well the ep1 part [spoiler]where you are stuck in that dark bit near the elevator, I found worked in the spook factor.[/spoiler]
But I agree with your earlier rant, about developers doing too much of this. Also I found that the guys at iD and Valve were trying to one up each other, possibly because they had released their competing engines at the same time.
While HL2 was all about physics, Doom 3 was about the lighting and how that added to the spook factor. Well in the Doom 3 expansion, they added a half assed gravity gun, that just didn't work without the physics of the source engine.
In HL2:Ep1 they added a total dark room level, with scarce lighting, as if to say "See, we have a bigger developer penis than iD."
While I liked it, I thought without the Doom 3 engine the horror factor didn't work nearly as well.