Queensland/Victoria
Great Barrier Reef, Fraser Island, Whitsunday Islands, Snowy Mountains National Park, the rainforested Daintree, Cape York Peninsula

South Tourism Australia
Grampians mountain range, fairy penguins at Phillip Island, gold-mining town of Sovereign Hill, Victorian Alps, Great Ocean Road

Sample Itineraries

Two weeks (with the train)
It takes three days non stop to cross the continent. A better route is the triangle between Adelaide, Sydney and Melbourne. In a cross continental journey, it will be nearly impossible to see Ayers rock in the north or the Great Barrier Reef in the northeast.

One month
Run up the east coast from Sydney to Cairns. Three months Sydney to Cairns and Darwin; Sydney to Adelaide via Cairns; Perth to Cairns; Melbourne to Cairns

Three months (with extended visa requirement)
East coast, Darwin, central Australia, Adelaide and Melbourne; Cairns to Perth via the southern or northern coasts.

source: Lonely Planet Publications and Bradt Guides