If you need to be formal or are talking to someone who is not a friend, stick with "How are you?" You can emphasize any one of the three words. I emphasize "are". It doesn't matter which one you emphasize, but you must emphasize one of them. Otherwise, it will sound like you don't really care what the answer is.
Other expressions I use:
"How's it going?"
"How have you been (lately)?"
"How have you been feeling (or 'doing') (lately)?"
"How 'ya doing?"
"What gives?"
"What's (or 'what's been') up (with you)?"