I wouldnt go as far as saying that HL2 blows Doom-3 out of the water. Both games are from completely different stables. Doom-3 is something you EXPECT to be a corridor game because this is the way it has always been. HL2 has moved out into the open which is a huge step in the right direction but this doesnt detract from the appeal of Doom 3.
Basically - Doom 3 does the job - gets you shit scared and shivering like the last leaf after the fall. HL2 is a thoroughly immersive experience where you can think and rationalize...resourcefulness etc. a better game overall but not by a huge margin if you just focus on what the developers set out to do.
I still rate Doom 3 highly. I just prefer HL2 and Far Cry.
Honestly - between HL2 and Far Cry it is a tie for me so far