It really depends on what sort of flying you'll be doing. You mention Emirates, however remember that emirates is not aligned with any major alliance, so chances are any points you earn with Emirates will have to be used to go to an Emirates destination.
Whilst Emirates is not aligned with major alliances, points can be credited to a range of programs. The most relevant for many Australians being Virgin Blue Velocity.
markm, to get a better answer to your question it is probably useful to provide some more information:
- how often are you likely to travel domestically and internationally?
- Credit cards - do you have/can you get and how significant is your spend on them (roughly)?
- How do you intend to spend points (free domestic flights, free international flights, flight upgrades, online shopping?)
For the infrequent flyer it can be often best to shop around and find the best fare, rather than pay extra $$$ for points towards a free flight that may or may not materialise in the future (eg if Emirates is offering a $600 fare and Qantas have the same destinations for $900 it's probably not worth taking Qantas just for the points).
If you fry frequently you should look into a range of options, and the best may depend on the mix of domestic and international travel you do and where you fly to - you should definitely provide more details to get some help here.
If you fly occassionally it may be best to look at either Qantas or Virgin Blue as both offer awards for domestic travel at fairly low rates and are linked to credit cards that can be used to top up the points you earn from flying. Also both have a range of international airline partners, although Qantas does
arguably have better availability with their international partners at lower points.
Lastly many of us here have prejudices/biases one way or the other when it comes to particular programs, be careful that whatever you read actually applies to your own situation. Oh and also - be wary once you start flying airlines outside Qantas/Virgin Blue/Emirates. Many other airlines (such as Thai, Cathay Pacific, Malaysian, Singapore Airlines, and most notably Jetstar) have low fares that do not earn any points on any program, just a caution (however with this in mind do reread my 3rd paragraph!)
Good luck!