Great question. Here’s some info to consider.
Option 1 - Qantas & Emirates
Emirates service Hamburg one-stop from Australia, and are the only airline to do so - but not with Premium Economy.
You could look at buying Qantas fares (via Qantas.com) to include service in Premium Economy to Dubai, and then onward with Emirates in Economy.
If booking through Qantas, you would earn Qantas Points which you can then top up with the Qantas credit card of your choice. You may a bit more than other airlines to book through Qantas.com but at least you’d earn points you can supplement with a credit card easily, and have the benefit of the 1 stop flight.
To note though - the connection time in Dubai for the outbound (connecting from Qantas’ A380 service with Premium Economy) is 9 hours, overnight. This could be a good or bad thing depending on your preference. The return is not so bad with a 2.5-3 hour layover in Dubai.
Option 2 - Emirates
If you don’t like the sound of that layover, then you can travel all on Emirates for a better connection - but with no Premium Economy. In this case you will have to check the price of booking with Emirates vs Qantas on the same flights. They should be similar, but worth confirming.
In this scenario - no Premium Economy at all, but good connections. And still just one stop.
Another Economy only option would be with Etihad and Air Berlin, one stop to Berlin, worth keeping in mind.
Option 3 - Cathay Pacific Premium Economy to Frankfurt
This is likely to be a good one if you are willing to pay for Cathay Premium Economy. It’s a great cabin - I’ve reviewed the Cathay Premium Economy Sydney to Hong Kong service here.
You would earn most points by accruing to Cathay’s own Asia Miles program. You could supplement the miles you earn from your international trips from domestic travel on Qantas into Asia Miles too (assuming you won’t travel too much domestically as the earn rates are not great), as well as topping up from a credit card from the Westpac Altitude Rewards, American Express Membership Rewards or ANZ Rewards ranges.
Asia Miles program is generally good for upgrades on Cathay Pacific flights too.
You could also look at British Airways to Hamburg via London - you would probably best also accruing this flight to Asia Miles as Qantas earn rates have gone down dramatically on BA last year.
Singapore Airlines also have plans to launch Premium Economy service to Frankfurt in December, in which case you would accrue Krisflyer miles and again look to supplement from one of the cards linked above, as well as from Citibank Rewards. I would imagine though that Singapore Airlines Premium Economy won’t be too cheap outside of their biggest sales.
Hope that helps!