Intonation and Its Parts

"It's not what she said, it's the way that she said it," is a complaint we have all heard (or made) some time or another. What does it refer to? It obviously relates to the various forms of wordless communication, but especially to the speaker's use of intonation--the rise and fall of the pitch of the voice--to convey sarcasm or resignation, anger or apprehension, or any of scores of other moods.