From native English speakers I often hear the phrase "How are you?" intonated differently. Sometimes the word "are" is stressed, and sometimes the word "you" is. What is the difference between these variants?
Typically, the first person to ask the question will emphasize the word are.
After responding, the second person will emphasize the word you to indicate that they are changing the focus of the conversation from themselves to the other person.
The exchange is often something like this (though the italics aren't typically written):
A: How are you?
B: I'm fine. How are you?
You is, as onomatomaniak says, normally only stressed in a reply. However, there are some particularly effusive characters who will stress you even when they are initiating the greeting.
Hi how are you (going up)
Hi how are you (going down)
Hi how are you
Hi how are you
...are all valid, along with 1001 other variations of the platitude (how are you doing, how's it going, how you doing). It makes no difference to the meaning but does change the emphasis slightly so the speaker is implying a different meaning.
But the main difference is between sounding like you care versus being polite.
The stress emphasises the questioner's focus.
"How are you" says "I'm not asking about anyone else. I am specifically asking about you."
"How are you" says "Let's take it as understood that I'm asking about you. The important thing is, how you are."
But, these are subtle differences, and the speaker probably isn't thinking about it when they speak.
Having recorded acres and acres of English languages courses over the past 20 years, and so having heard (and recorded and directed) many people say "!How are you?" (obviously a classic phrase to learn at beginner level) I think I can assert that the classic "How ARE you" as an opener, followed by "How are YOU" as a response (which I also taught for years) is no longer true in all cases. Many if not most younger people say "how are YOU" as an opener these days: the stress on YOU seems to indicate friendship, and is used to show that they are talking to and enquiring after "YOU". In fact, if you ask some young people to say "How ARE you" some of them giggle - they think it sounds funny and a bit high class. However the old pattern is still true for older people - 40 and over I'd say - although that's changing too. None of which makes life any easier for the teacher of English - or the learner, of course.