'How are you?' is the most common way, but the least emphatic if you ask me. The person doesn't normally take it seriously and say 'Oh, you know I don't feel alright etc etc'. 'Howdy?', 'How have you been lately?', 'How is it going?' etc are some other examples.
If you are really close to the person, and you want the person to know that you care about them, then the best way is to ask a direct question.
Some examples:
1. How is your health now?
2. Have you been busy with work lately?
3. Did you find time to watch that movie?
All these questions mean the same thing 'How are you', but in a more meaningful way, to which the person can reply to.
Cheers.