Formal:
* To which you refer?
* Which do you mean?
* Which one are you talking about?
* Could you clarify which one you are referring to?
Informal:
* Which one?
* You mean this one?
* What are you talking about?
* I'm not sure I follow, which one?
More specific:
* Which topic/point/argument/idea/option are you referring to?
* Which of the choices are you considering?
* Which statement/quote/passage are you referring to?
The best option will depend on the specific situation and the tone you want to convey.