I have Cilla Fisher and Artie Tresize's version (from Foul Day and Fair), which ends "When the captain did behold her and the deed that she had done/he has made her chief commander over a ship and a hundred men", which is the first version I had ever heard. I also have Robin Williamson's version, which goes "when the captain heard of this and the deed that she had done/he made her a ship's commander of a frigate of thirty gun" (that's from A Job of Journey Work ). I have a version by Arcanadh that ends with the shooting, and one by The House Band which has the version ending with "if all young ladies did t he same, how many less young men there would be". I know I have more at home, but those are the ones I have on the ipod at the moment.
The Versions of "Willie/William Taylor" I know