Precious few trains exist to service heavy hauling needs in the Equestrian Wasteland. Where both a working train and intact tracks still exist, trains operate much as they did pre-event. A coal-powered engine (sans coal) headed off a series of purpose-built cars: Flat and box cars were used for supplies, passenger cars carried ponies, and the caboose housed the brakes for controlling speed down hills and ultimately stopping. A team of puller ponies, typically Earth Ponies, acted as the locomotive.
Most trains operate with a brace of defenders to discourage or protect from raiders. For routes that require extended climbing, a second team of puller ponies will rotate pulling and guarding duties. One or more Unicorn switch pullers are usually present.
It was suggested in 'Project Horizons' that some locomotives were adapted to run using specially adapted magic talismans. It was also suggested that these locomotives looked nothing like its coal burning cousins, and so presumably looked comparable to Real-life diesel/electric powered locomotives. Although not mentioned it can be assumed that locomotives powered by alternative fuels were being developed: presumably this project would be headed by the Ministry of Wartime Technology (Maybe in partnership with the Ministry of Arcane Science) or Equestria's railway operating division.