Travelling in Australia

Airlines and Bus companies

Qantas - national airline
Virgin Blue - domestic airline that offers quality service and value for money. Daily happy hour specials
Jetstar - budget domestic airline offers very cheap flights to main capital cities often using out of town airports Greyhound Pioneer -  interstate bus services for all states
Firefly Express -  daily services between Sydney, Melbourne and Adelaide  
Railmap Australia - a map of Australia's rail systems and links to various state railway sites

Tour Companies

National tours
Adventure Tours - small group, nature-based adventure tours 
Groovy Grape - eco-certified tours of southern and central Australia
Wayward Bus - budget small group tours between Melbourne, Adelaide and the outback
Oz Experience - backpackers travel company that offers travel passes and tours around Australia

Tasmania
Under Downunder - small group that offers budget eco-certified tours of Tasmania
Bottom Bits Bus - small group budget tours of southern Tasmania
Island Escape Tours - offers 1-7 day tours and a hop-on, hop-off bus service

The Outback
Wayoutback Desert Safaris  - small group 4 wheel drive tours (7-14pp) of Alice Springs and Uluru
Travel North - offer several tours from Darwin and Katherine visiting Kakadu and Litchfield National Park

Western Australia
Easyrider Backpacker Tours - tours all over Western Australia and into Darwin, also offer a jump-on, jump-off service

The East Coast
Intrepid Tours - excellent independent operator, offers a number of tours from Sydney to Cairns
Sand Safaris - very popular 2-3 day tours of Fraser Island
Autopia Tours - tours leaving from Melbourne exploring the Great Ocean Road and Phillip Island, eco-certified

Destination Information

The following government tourist offices provide detailed information about travelling in each state. There are also useful tools like maps, itinerary planners and event guides. They are a great place to begin planning your holiday in Australia.
New South Wales  
Canberra
Northern Territory
Queensland
South Australia
Tasmania
Victoria
Western Australia

Accommodation While Travelling

Hostels & Hotels
YHA Australia - over 140 YHA hostels in Australia
Hostelz - website that gives detailed reviews of hostels
Tripadvisor - detailed reviews and forums for posting questions

Last Minute Booking Sites
These sites are great for finding hotel accommodation for booking in the next 2 weeks often for half the regular price.
Need it Now
Last Minute.com
Wotif
Hotelclub