We are due to sail on the Mercury in January 2008 and yes the travelling is the one thing that well you have to live with. There is an option possibly of looking at an overnight stay en route in Singapore or possibly look to upgrade your accommodation on the flight. There are special socks you can wear as well but I find taking a walkabout when possible and riggling my toes are two other options. On our trip we fly to Sydney to join the ship and fly back from Auckland to Sydney then onto London, but I think we might sleep a fair bit of the flight but time will tell.
 Upgrade to World Traveller Plus/Business for more leg room  have a stop over in HK or Singapore so you split the journey into 2 managable 12hr sections, this also gets you over the first hurdle of jetlag  adjust your watch/body clock to the timezone and try and eat/drink according to that time to get you acclimitised. I've flown there tons of times - contary to what they advise - I drink as much wine as possible and tend to sleep a lot.
I've made the trip to Australia 4 times and would strongly recommend breaking the journey with a stopover in both directions. It not only breaks the time you are stuck on the plane but also helps you adjust to the time difference so that you can make the most of the cruise when you get there instead of feeling worn out for a few days. bangkok, Singapore and bali are all fascinating places to stop and are offered by most airlines as stopover options. Whilst on the flight - don't eat too much - it's very tempting to eat all the meals they bring you because you are bored - but only eat when you are hungry and go for the lighter options. Avoid alcohol and drink lots of water. Try and get aisle seats so that you can go for a walk evry hour or so. Instead of getting the steward to bring me water, I always walk to the water dispensers to get it, so as to keep moving. Some people recommend taking an aspirin before the flight but I've never had any problems myself with long haul flying other than getting bored and a bit stiff. Whatever you do, dont let worries about the long flight put you off going - australia and new Zealand are fantastic countrie.