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.
In western Europe, the train is by far the most popular public transport.
For trains any discount found on tickets on the official site can be purchased with credit card and sometimes with Paypal. The transactions are usually in foreign currency (Euros and Swiss Francs in my case) so typically banks charge 3% service and the Paypal exchange rate works out to 2.5%.
Tickets I purchased from Tren Italia while in the United States were charged in US Dollars using a rate calculated by Tren Italia.

For buses, we have usually gone to the bus terminal a few days before and bought tickets. This worked well in the Baltics and continues well for Trieste day trips.
I have not found the iPad apps so useful for purchasing tickets. For checking schedules they seem to work pretty good.
I use two Swiss Train Apps:
and

These two apps not only show the train schedules, but also the post bus schedules that run through villages.
The problem with most official travel websites is that they want to promote their best fares. These are not necessarily the cheapest. For trains, usually, local trains are very good options for shorter distances when time is not a major factor. An example of this is from Lugano to Milano. Taking the the regional S10 to Chiasso and transferring to the S11 to Milano Porta Garibaldi stations is about half the price. Sometimes the website will not show these connections out of central stations. Looking for schedules out of smaller stations, such as Lugano-Paradiso, usually reveals the schedules. Usually, tickets can not be purchased in advance. Switzerland and Italy now have ticket machines that dispense current tickets, day passes, discounted tickets in several languages.
Getting Around the City
Like the national train lines, most major cities have websites for local transportation. We have used these extensively last year in Riga, Tallinn, and Helsinki. Google translate comes in handy as frequently the website is only in the local language.
Here in Trieste, I use this website in Italian:
In Lugano, there is: