Well you did ask which OW airline program you should join..
Your choices for Australian Domestic are Qantas and Virgin, neither of which are Star Alliance.
If you are going to be flying Emirates long haul, then Qantas is the obvious choice of program for any OW travel because of the tie up with Emirates. Although full details haven't been announced, you should be able to get FF points credited to Qantas when flying Emirates.
But then you've got to start from scratch with them, so i guess internationally, i should just stick to *A and domestic just fly any one of them.