What is best method of transport from Prague to Salzburg ?
Train to Linz then change for train to Salzburg. Second option - bus. Or private shuttle door to door. It depends what you mean by the word best. Fastest? Cheapest? Most comfortable?
The train combines economy and comfort. Bought well in advance tickets can be as cheap as EUR 24,90 (less than USD 30). Consult the railway agent Loco2 for schedules and tickets.