Train: Munich to Prague

The fastest (~6 hrs) train connections from Munich to Prague are regional trains. There are no reservations required or possible. You can buy your tickets in Munich. One of the best ways is to buy a Bayern-Ticket in Munich. It will give you unlimited travel in Bavaria, to the Czech border, for €19 for one person, €27 for up to five people. Also buy in Munich, Anschluß tickets for everyone in your party for the German-Czech border to Prague, about €20 per person.

You can read more about it here.

The Bayern-Ticket is only valid in 2nd class. Most people think 2nd class is good enough.

Personally, I would never buy a ticket before I left the states. We did have our Rail Passes.

We traveled for 8 weeks..when we arrived in a town we bought our seat reservations for our departure. The ONLY time the seat reservations paid off was the train from Zurich to Salzburg. The 1st class cars were full for a portion of the trip. Even then we could have sat in the smoking section in 1st class or couch.

If you want to purchase ahead of time, you can do so at the German railway website, bahn.de (switch to English in the upper right corner.) Prices start at about 54 Euro but, as Larry notes, you might want to wait until you get there to use a Bayern Ticket to the border, then purchase another one for the rest of the journey. BTW, with a rail pass, many fast trains in Europe REQUIRE additional reservations, so it's not a matter of whether it pays off or not....they're necessary before you even board the train, no matter how empty it may seem.

I didn't pre-purchase any tickets prior to my trip and just bought them at the train station (I did the reverse - Prague to Munich). It's pretty easy to do so and when i did research it was cheaper to just buy individual tickets for my destinations as opposed to a rail pass. (But I was hitting 3 specific cities as oppposed to hopping on and off so if that's the plan it may be more cost-efficient to buy the rail pass)