Instead of baking-in stopovers in your search (which might take you longer - and result in you losing out on a booking), you may want to consider the Virgin Blue Airpass. Not sure if it nets out any cheaper / more expensive though ....
http://www.virginblueairpass.com/
Prices are in
Australian Dollars ^ - which are at a 5 year low against the US Dollar:
http://finance.yahoo.com/echarts?s=A...urce=undefined
with the Virgin Blue Airpass you can create your own Airpass travel plan for as little as A$207* for 3 flights in Australia.
It’s easy, all you have to do is choose a minimum of 3 flights across any of the four Virgin Blue Fly Zones*:
· Quick Fly Zone fares from $69* per flight
· Metro Fly Zone fares from $79* per flight
· Coastal Fly Zone fares from $99* per flight
· Cross Country Fly Zone fares from $179* per flight
These great low fares are available all year round, with no season restrictions!
No minimum or maximum stay in Australia applies, and there are no change fees for extensions or flight changes^.
* Offer valid with any international air ticket to Australia.
Fares are in Australian dollars.
http://www.virginblueairpass.com/airpass/Search.jsp