Bruce: The money was stolen, you tell me, John. Well, I don't think Molly took it.
John: But then, who did take it then?
John: But then, who took it?
Summary: In John's question who did take it is used instead of who took it. The use of did take is used to emphasize the fact it was taken.
The implicit suggestion is that previously in a conversation someone has said that some person did not take it. It is a way of being more emphatic.
Do can also be used for emphasis:
If you don't do laundry for us here, who does do it?