We are considering the Best of Eastern Europe tour next September, and we're thinking about flying into and out of Munich, then taking the train to Prague. We love rail travel, and would arrange the extra time and lodging needed to add this to our trip itinerary. We'd finish the RS tour in Lubljana, Slovenia and take the train back to Munich to catch our outbound flight. Has anyone done anything similar? We live in the Twin Cities, and Icelandair flies out of here with great prices to Munich (as of now anyway!).
My wife and I did this tour three years ago (loved it!), and took the train to Munich from Lake Bled afterwards. (The tour actually ends at Lake Bled.). There's a small station right on Lake Bled, but it's not the one to use. We, and many others from our tour, took the short taxi ride into the town of Lesce, to the Lesce-Bled station. It's on the train line that runs directly between Ljubljana and Munich. From Lesce, the ride was about 5:30 hours, so add about 45 minutes more if going from Ljubljana. As the train ends up in Germany, I was able to buy our tickets online from the bahn.com website, and took them with me. If you have time after the trip, Ljubljana is definitely worth a couple of days.
Go the Deutsche Bahn website to check schedules. Currently the last available date is Dec. 10, which may be far enough out that you can determine what the lowest early-purchase fare would be. If not, more data should be loaded very soon, and you'll be able to check dates farther into the future. The lowest Savings fares do not allow cancellation or changes, so be very sure you know when you want to travel before buying the tickets.
There appear to be 3 trains per day from Ljubljana to Munich. There is also bus service, which is what I used last year. If something untoward occurs and you need to buy tickets close to the day of the trip, the bus could be far less expensive. The GoEuro website lists the bus options.
I see a lot more options to Prague, many of them being partly or entirely by bus. Again, you can see the schedule on the Deutsche Bahn website.
The fastest way from Munich, downtown, to Prague is the IC bus, which takes about 4½. It's a nice, modern over-the-road coach with a WC, snack bar, and attendant. However, most runs are non-stiop to Prague; you have to go into town on the S-Bahn, to the ZOB (Zentrale Omnibusbahnhof) at Hackerbrücke to board the bus. That backtracking makes the trip over 6 hours. Of course, if you are going to spend a night in Munich before going on to Prague, that would change things.
With a purchase far enough in advance (92 days max) you can get a 2nd class fare on that bus for as low as 14€/P. However, that fare is for a non-refundable ticket valid on that particular bus (date and time) only. If you are planning to use the bus just after arrival by plane in Munich, that is a bit risky. A flexible, full fare ticket for that bus connection is over 72€/P. That's why I only recommend it if you are spending the first night in Munich and can reliably catch the specified bus.
An alternative to the bus would be one of the ALX (regional) trains the go from Munich Hbf to Prague four times per day. One that leaves Munich Hbf at 12:44 stops at Freising at 13:09. You can get to the Freising Bahnhof by bus (about 20 min). With a Bayern-Ticket, 28€ for two people, you can go from the airport to Furth im Wald by bus and train. Then use a Czech Rail ticket for two for 662 Kc (about 24,50€) to go from Furth to Prague. You can purchase that ticket online from www.cd.cz (will displayin English).