What did you say? = 너 뭐라고 말했어? I think my answer is fit to your intention. ^^

We say 뭐라고 하셨어요? most of the time, it's the honorific version of 뭐라고 했어? You could say "저, 죄송한데, 뭐라고 하셨어요?" if you're looking for something so polite that people think you have a very good education.

무슨 말이었어요? Is just polite. Which literally means what say. Or 무슨 말이었습니까? This is the honorific form. But people don't use honorific form that often.

뭐라고? and 뭐라고요? is used when you are kind of angry at what the speaker said. It's "what did you say???" The expressions in each answers except the first one are correct. But I strongly suggest "실례지만, 다시 한번 더 말씀해 주시겠습니까?". It means "I'm sorry (or excuse me), could you say that again?" I'm sure the expression is quite formal and proper when you want to listen again and to know what the speaker said exctly.

"말씀" is a honorific form of "말", so the honorific of the sentence would be "뭐하고 말씀하셨습니까?" or "무슨 말씀을 하셨습니까?" \^o^/