I had to pick Parce mihi domine for the first one, largely because that scene has the most emotional impact on me, regardless of the music. I'm not sure I can separate the effect of the song from the overall effect of the scene.
True Faith has always been a personal favorite, but I find it interesting that songs that I liked waaay before I ever heard them on QAF have now become so closely associated specifically with QAF whenever I hear them.