Booking flights is a painful process. Fares can vary wildly depending on your booking date, when you're flying, what time you're flying, and more. It's often tricky to compare lots of airlines at the same time to find the best deals - this can mean thousands of dollars of difference.
Flying from Australia means that layovers are often inevitable. Ensuring adequate transfer times (and minimizing overall layover time) can also be aggravating - particularly when there are multiple layover options with different airlines servicing different hubs.
I've found a few sites that help make this whole process easier. Hipmunk is a general flight and hotel search website that seems to pick up just about every flight possible for searches. It has a great interface that lets you visualise costs, flight times, and layover lengths. This interface is absolutely streets ahead of anything else I've ever seen for flight searches, with great use of colour and space to convey the information. It also includes direct links to purchase tickets for the flights you choose - very handy when the flights are with multiple airlines.
Hipmunk gets its data from ITA Matrix. While this site isn't as pretty as Hipmunk, it is substantially more comprehensive. Hipmunk will only let you search for flights with a maximum of 3 legs; Matrix will handle an arbitrary number of connections. Matrix also presents many more flight options and perturbations than Hipmunk seems to, allowing more flexibility in travel times.
Unfortunately, Matrix doesn't include links to purchase tickets, or search for hotels. This isn't too bad when all the flights are with a single airline, as you can go to that airline's website and do the booking there with the flight information Matrix gives you. However, for flights on multiple airlines, this means taking the flights that Matrix produces, and either using a travel agent, or tediously trying to track down the flights on other travel sites. This isn't quite so nice, but when you're optimising at this level I suppose it's much of a muchness.
Finally, many airlines let you choose seats at booking or check-in. SeatGuru is a great site that describes each airline's fleet, and the seats to try for or avoid on each plane. There's also airport information, details on in-flight amenities and services, and a wealth of travel tips. It's a convenient way of making sure you don't end up with a terrible seat for a long, long flight.