Hi Dave.
Most of my diving is based around Melbourne where I live, however if you're in Australia and can get up to Queensland then of course the Barrier Reef is The iconic place. My wife has dived on the Yongala and rates it as the best dives she has ever done, however I believe that it can be a tricky site to get on to as conditions have to be just right.
I think the main thing to bare in mind is that without stating the obvious, Australia is a big country, so unless you want to spend most of your time in airports I would limit yourself to the East coast. Sydney itself has many excellent dive sites, for example Magic Point for Grey Nurse Sharks (need to check the time of year though as they are seasonal) or even Shelley Beach for an excellent shore dive. Byron Bay has a good reputation. My personal recomendation would be Southwest Rocks. Most of the diving takes place at Fish Rock, an island just off the coast, a 125m tunnel leads right through the middle of the island and if that doesn't keep you interested there are the Grey Nurse Sharks, Wobbegongs, Stingrays and Queensland Groupers :-). I've dived with them before and will be going back later this year.
http://www.southwestrocksdive.com.au
Dive Oz is also a good source of information for anyone interested in diving over here
http://www.southwestrocksdive.com.au
Wherever you pick though you're sure to have a blast.
Tony