How do you say 'how are you doing' in Japanese?

There are two ways depending on who you're talking to.

If its someone of respect, it would be お元気ですか (ogenkidesuka)

If it's someone you know or in the same 'social ladder' it would just be 元気ですか (genki desuka)

you do not need to put a question mark because the ka at the end implies that it's a question. =]