The music as seen at the end of the QL, the church scene, the city bits, and the very end of the game are all awesome, and the low temperature containment and sluice gate sections deserve special mentions as well.
I didn't realize that I was suffering from graphical errors throughout my play through. I only watched videos after completing the game, and I think coloured fog was brightening the game for me. The piston room looked amazing and scared the shit out of me, because it was one of the few places that was very dark and lacked fog.
Check your drivers and settings if things look funny at all at the start of the game!
I had the same change from fear into grim determination 3/4 of the way through. I am certain that this was intentional.