Across Australia by train
Australia is crossed by two great railway journeys, The Ghan, which crosses north to south straight through the heart of Australia, from Darwin to Adelaide and the Indian Pacific which crosses east to west, from Sydney to Perth.
The Ghan is named after the Afghan camel trains that used to service the Outback, construction on the original Ghan from Adelaide started in 1878, with Oodnadatta reached in 1891 and, after a thirty-year break, Alice Springs in 1926. A separate but unconnected track from Darwin to Katherine in the north was also completed in the same year.
Unfortunately, the original Ghan was twisty, narrow-gauge and built straight through many valleys prone to flash floods that washed away tracks and bridges. A decision was thus made rebuild nearly all of the line in standard gauge, over 100 km to the west. The new line to Alice Springs opened in 1980, and the remaining 1420-km section across the continent to Darwin opened in 2004.
This isn't a high speed transcontinental railway. This is a laid-back kind of train that knows how to take its time and enjoy the scenery. The trains are privately run by Great Southern Railways .
Any way you look at it, the Ghan and the Indian Pacific are expensive, unless you purchase a Rail Pass . The standard "Red Service" Daynighter reclining seat is $716 from Darwin to Adelaide, although the price is cut in half if you book a prepaid, non-refundable, non-changeable "Rail Saver" fare or use a child, backpacker or YHA fare. A "Red Service" twin share sleeper cabin is $1312/800 standard/concession per person, with no Rail Saver available. Don't expect luxury: the trains used are refurbished 1970s-vintage American models.
If you fork out $1973/1357, you can upgrade to "Gold Service", which has single cabins (shared shower), twin cabins (shower ensuite) and includes all meals in the dedicated restaurant car. Add another $1000 on top, and you can get a double-sized "Platinum Service" cabin.
If you have a car in Australia, the value proposition can improve slightly, if you take your car with you. On the premium fare there are often deals available to take a car for $99 extra, which you can the offset against the price of renting a car at your destination, or if you drive one way, the prospect of the 3000km drive home.
You can also leverage some value out of taken stops at the destinations along the way, with Alice Springs being the perfect stopping point on the Ghan, and Broken Hill and Adelaide both being good options on the Indian Pacific. There aren't too many other options, though, with small towns, infrequent service and inconvenient arrival times making the other towns a hassle to stop at.
If you have a non-Australian passport, you can purchase a Rail Pass and save a considerable amount of money. The Ausrail Pass  ($722 for 3 months, $990 for 6 months) allows unlimited travel on "all long distance services in any direction as often as you like over a six month period" . The Ausrail Pass is only valid for Red Daynighter Seat/ Economy Class. If you only want to explore one part of the country, there are other passes available for even less money that cater to specific sections.
Sydney, Perth and Adelaide are well-connected by air, each with services to all other Australian capital cities and international destinations. There are public train services up and down the east coast connecting through to Sydney. There is a public train once a week to Broken Hill, which you can catch from Sydney, and then join the Indian Pacific there. This trip costs considerably less than the privately run Indian Pacific on the same route.
This itinerary assumes you start from Darwin and head south, but obviously it's also possible in the opposite direction.
From Darwin (0 km), there is a departure every Saturday (9 AM) throughout the year, and an additional service on Wednesdays (10 AM) between May and October. The three-day, two-night journey takes around 48 hours from end to end.
The station is a fair way from central Darwin, about 20 minutes drive. The railway's primary purpose is freight, and the line goes straight to the port at East Arm, without passing through any built-up areas. Dedicated buses connect between the Darwin Transit Centre in Mitchell St and the rail station for an additional fee. Taxis are possible, but expensive. There is no scheduled bus.
From Adelaide (2979 km), departures are on Sunday 12:20 noon throughout the year and Wednesday at the same time between May and October.
Katherine (312 km)
The Ghan stops here for around five hours, with an optional guided "Whistle Stop Tour" available.
The old Ghan railway from Darwin to Katherine stopped in central Katherine, and is now a tourist attraction. You can walk the old high level railway bridge across the Katherine river following the old alignment. However, is around 10km from the old station to the new one, so if you want to see Katherine, the tour may be your best option.
Tennant Creek (945 km)
Passed through in the middle of the night in both directions, stops only on request.
Alice Springs (1420 km)
Alice Springs is the former northern terminus of the Ghan and the largest town by far en route. The train stops here for around four hours, long enough for a quick peek around town. The station is on the edge of downtown, a couple of blocks walk to the Todd mall. Many people opt to break their journey here for a few days and visit Uluru, about 400 km away, but there is plenty to do for a few days in Alice and surrounds even if you don't venture to the Rock. Alice Springs has all the services to make it possible.
Is a roadhouse in the desert.
Chandler is a tiny settlements where the the Ghan intersects the Stuart Highway. Marla is a purpose built highway service centre with nothing else there except the highway, train line and the station. The highlight of any visit there is to see the Ghan when it passes through, and the desert stretching off into the distance, if you are actually on the Ghan looking at the desert stretching off into the distance, best to stay on board.
If you do decide to get off, the motel, service station, and associated facilities are just across the road from the station.
Coober Pedy (Manguri)
By prior arrangement only, the Ghan can stop at Manguri, 42km away from the town of Coober Pedy. You must have prearranged a pickup from here, since the location is very remote.
Markets itself as a "seriously outback town". Small town with just a pub. The train can stop here with prior arrangement, and the station is just across the road from the town. The Kingoonya Waterhole Hotel  is just a couple of minutes walk from the station and accommodation is available.
You can catch the train at Pimba with prior arrangement. Woomera is just 6 kms away from the station
Railway buffs may wish to get off here and ride the Pichi Richi Railway  78 km to Quorn, running along the original Ghan track and using original Ghan equipment. Departures are limited, especially outside the winter season.
The station is in the suburbs, around 5km from the town centre. The old station in the centre of the town is closed and is a museum, including many items of railway heritage.
Adelaide (2979 km)
The Indian Pacific
On a connecting train
The Overland train (which is also a Great Southern Railways private train) also runs to Melbourne, although that 10 hour journey lacks some of the spirit of the Indian Pacific or the Ghan.
There are no interstate public trains that run into Adelaide.
And see what you missed
Australia's pioneers had a grand vision for the railways, to cover a continent, and there are many places where this grand history can be seen. If you are catching the train one way, and travelling the other way, you can catch up with some of the interesting railway history you may have missed.
The town of Peterborough is well worth a stop - the town was built on crossroads of the Australian railways. In Indian Pacific stops there at night, and doesn't do the town justice.