We just got back from a trip that started along the Rhein, then Berlin, Dresden, Prague and Vienna. We traveled by train, second class. We booked most of our tickets using the Deutsches Bahn website, no problems with printable PDF tickets or using American credit card over the web. The Prague to Vienna ticket we did thru Austrian Rails website (OBB), again no problem. We paid for seat reservations when they were available. All of the train tickets for two people added up to about 220E. Would have been less if we hadn't delayed purchasing the Rhein to Berlin ticket. When we first looked, it was around 50E, a couple weeks later I paid 80. Live and learn.
We had a few issues. We left Bacharach early on a Saturday figuring we would stop off in Mainz before going on to Frankfurt and getting on our ICE to Berlin. The Regional Express from Bacharach to Mainz was on time but had quite a few well lubricated soccer fans. We ignored their singing and got to Mainz okay. After a couple hours there we went back to the station to get the RE to Frankfurt. The 10 minute transfer time in Frankfurt for ICE to Berlin didn't allow for the RE to be 10 minutes late getting to Mainz where it disgorged a whole lot more soccer fans. Late leaving Mainz, and we just missed our train in Frankfurt. DB gave us new seat reservations for a train that left an hour later, so we arrived in Berlin later than we wanted but not too bad.
Berlin to Dresden, Dresden to Prague, Prague to Vienna. Each of these trains was really full, especially Prague to Vienna. We were very glad we had seat reservations. Folks who didn't had a hard time finding places.
Berlin to Dresden - Didn't quite figure out which end of the car to get in, and it had compartments with a narrow aisle. It is quite a scene when you have people going in both directions with lots of luggage trying to get past each other looking for their compartment.
The skinheads on the train from Dresden to Prague were somewhat annoying and when one of them answered his phone with "Heil Hitler" I felt a little ill. The route along the Elbe from Dresden was beautiful with tree covered mountains and your occasional castle.
Prague to Vienna - Boarding this train was total chaos, though I did manage to find the correct end of the coach to enter. People without reserved seats were scrambling trying to find a place. It is a long ride but with some pretty scenery.
The trains from Berlin to Vienna were all Czech railways. Prague to Vienna was Railjet, but really just Czech rail train.