It is very commonplace to just say, "What?" However, that is something you should use only with someone familiar to you. In a more formal setting, or with someone you need to regard with professional distance, you might instead say "pardon?" (especially in the UK I think) or "once more, please?", etc. Rob's answers are correct too of course.

Saying ‘pardon’ is good. I’d say that it is not outdated. Alternatives: “Sorry, I didn’t catch that…” “Sorry, I didn’t hear that” “Sorry?” “What did you say?” “What was that?”

Please? Once again?

Could you please repeat that?