I want to travel from Sydney through Bangkok, Phnom Penh and Ho Chi
Minh city and back again, in any order. Probably want to go at the
time of year that it is cheapest, probably looking at doing it over a
two week period, and prefereance is over the christmas break or near
publi holidays. I am happy with any mode of transport, but looking to
do it on the cheap, maybe train, maybe bus. I would like to know costs
of travel, modes of travel available, where I would book it or how I
would pay for it all.

If you are going to Cambodia, and are at all interested in the history
of the region, you should consider visiting Siem Reap, where a large
number of Angkor temples (including Angkor Wat) are located. I know
somebody who took a boat up the Mekong from Ho Chi Minh City to Phnom
Penh - but it would probably be less expensive to fly.

You have a travel agency in Australia which books tours in Southeast
Asia. I once took a tour through their "Peregrine Travel" division.
They also operate "Gecko's Adventures", which offers lower priced
packages. You may wish to explore their sites for travel ideas.
http://www.peregrine.net.au/
http://www.geckosadventures.com/

The following page might be of interest:

Travel to Provincial Cambodia
http://www.canbypublications.com/miscpages/provtrav.htm


Search terms:
"travel route" "Bangkok" "Phnom Penh" "Ho Chi Minh"

just a comment that it's probably cheaper to fly from Sydney or
Melbourne direct to Bangkok or Singapore or somewhere, than the try to
do part of it overland (ie, tourist flights to Asia often cost more
from Darwin).   There are many flights from Sydney or Melbourne to
Bangkok or other popular destinations.  Flight centre
(www.flightcentre.com.au) has cheap flights.  Sorry I haven't done
enough of SE Asia to help you with your actual question about travel
through SE Asia, though.