Here is a memory dump of some of the tips and tricks on European travel. These come mainly from my current trip so they are centered around Switzerland and Italy.
First of all the Internet is the go to place for searching and booking travel.
Train / Bus travel between cities
Almost all the train companies and bus companies in Europe have official websites. They usually have several languages, English be the most common alternative. Here are two examples:
For Buses, my favorite website is:
Eurolines just goes all over the place. These long distance buses result in some off hour departures and arrivals. Last year in Lithuania we boarded a bus that dropped us off in the evening at Daugapils, Latvia and then continued on to Moscow.