I prefer rail to get between cities.  Assuming you have a reasonable route, it’s the fastest, most comfortable and most convenient way.  If you’re in Western Europe, rail service will be significantly better than bus service.  If you want to explore a particular rural area then rent a car for a few days, but rely on the train for most of your intercity travel.  If some of your cities are far apart then look for a couple of cheap flights to save time and maybe money.

While train is the best way to get around, a eurail pass may or may not be a good deal depending on your itinerary.

I’d go by trains unless its a long disance in which case that a flight with Ryaniar.  One of the good things about taking a train that people often overlook is that stops are generally in the middle of downtown.  I think a pass will amost always be a good idea, but its usually better to underestimate and get a cheaper pass than get a pass you won’t use completely.  There’s a good chance you’ll cut places out of the trip.