The best, but most expensive airline is Qantas - they fly direct between Sydney and Manila.
Philippine Airlines also flies direct, however you have to be careful not to get on a flight via Melbourne or Brisbane (which is the case every other day). A stopover may be the last thing you want after an overnight return flight :)
Malaysia Airlines occasionally has cheap fares, however often the stopover in Kuala Lumpur can be inconvenient. On the upside, MAS also flies from Kuala Lumpur to Cebu (via Kota Kinabalu) every few days, so if you don't want to stop in Manila, this may be an option.
The cheapest is AirAsia, especially when they're on sale. Currently they fly out of Gold Coast and Melbourne, however they are proposing to launch out of Sydney on 1 June. AA flies direct to Kuala Lumpur LCCT, from which you can fly to Clark (Manila) via AA, Manila or Cebu, via MAS or Cebu Pacific. Note that the daily Cebu Pacific KL - Manila flight is cheap, but badass red-eye, departing at 1:20am.
A rival budget option is Viva Macau, direct between Sydney and Macau. You can then catch Cebu Pacific to Manila or Cebu.
Entry points into the Philippines are usually Manila, Clark field (often also known as Manila) and Cebu. Note that Clark field is about 2 hours out of Manila city and doesn't have much going on except a mall and a few duty free stores. Also, a lot of Cebu flights fly via Manila, anyway.
Here's all the airlines you need:
AirAsia - http://airasia.com
Cebu Pacific - http://cebupacificair.com
Malaysia Airlines - http://malaysiaairlines.com
Qantas - http://qantas.com.au
Viva Macau - http://flyvivamacau.com about 10 years ago