I am needing to get from Munich to Prague this September to join the Rick's Eastern Europe tour and am debating between the train or bus. I have seen a few comments on web sites that the train is the way to go but Rick's book says take the bus. Does anyone have any experience on either one? Any comments would be helpful.
The Munich to Prague bus is definitely the fastest (by 1½ hr) way to get to Prague, but it might be a lot more expensive.
The standard (full fare) for the bus is 66,20€ per adult. With sufficient advance purchase, you can get a Saving Fare of 29€ per adult, but you must book early, as much as 92 days in advance. The ticket is for a specific bus and has a penalty for refund (non-rufundable on the day of travel).
On the other hand, there are three direct trains per day to Prague, leaving Munich at 9:01, 12:44, and 17:02. With a purchase-at-the-time-of-travel Bayern-Böhmen-Ticket (25€ for one person, 29,50€ for two), you can travel from Munich to Pilsen. From Pilsen to Prague, you need to purchase a Czech Rail ticket to Prague from the conductor once you are in the Czech Republic for 100 Kc (about 3,65€).
I already answered your question under Czech Republic.