I don't think that Qantas vacations.com is actually the Australian airline, but simply a US travel agent that specializes in Australia.
Three thoughts.
1) australia.com Pretty good smattering of vacations (whihc might be cheaper than seperate hotel/flight)
2) use travelocity's fare watcher feature for melbourne, sydney and cairns
3) check out UA's buy two tix get one free deal. You could take two SFO-JFK runs and get a free systemwide ticket. I'm doing it in hopes of using the ticket to go (back) to oz from BOS
here's the forum topic in UA's forum
http://www.flyertalk.com/forum/Forum50/HTML/025212.html