Besides websites like expedia, orbitz, etc I find it handy to keep direct links to the airlines, both for searching flights and to print boarding passes before travel. Here are some of the major ones:
In a 2005 trip to Europe, Mary used the train sites in Switzerland and Italy to plan her trip. With accurate time tables, it was very useful for advanced planning. Google trains in the country you are going to and you will probably find something quite useful. Buses were a little trickier to find in advance.