Another is when GLaDos tries to incinerate you. The music is sharp and dreadful, kind of like a techno Snidely Whiplash moment.
The final moment I really noticed the music was during the climatic battle after you burn away her Moralty core. It is your standard climactic moment music.
Now this serves two purposes. The first is the lack of music. This gives the environments already sterile and solitary feel even more alienation. The second, in my opinion, is to give GLaDos a flare for the dramatic.