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I've actually found traveling buses between Central European cities to be easy and efficient. Try checking www.eurolines.com for prices. Many Americans have stereotypes about travel by bus, but I've found Eurolines coaches to be clean and quite nice. Plus, buses are often faster because they stop at fewer stations. I've travelled by bus from Prague to Munich, Bratislava, and Budapest, and would recommend that over travel by train (which I did to Vienna). Round trip tickets to Munich (with a youth rate) were under $50. I also like taking night buses. That way, you have your hotel covered for a night, and you don't miss any time during the day. Travel between Prague and Munich/Budapest/Vienna is perfec this way, when you leave at midnight, you arrive between 5-8am. I'd book ahead.
I also took buses to some places around the Czech Rep and found it fast and easy. Pus travel to Plzen (home of Pilsner Beer) was only about $10 round trip, and we bought tickets right at the bus. For domestic westward travel, however, be aware that you might have to leave from Zličín (last metro stop on Yellow line) instead of the main one at Florenc.
Hope this helps!
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