We recently went to Prague (along with Germany - full trip report under Germany forum) and figured this will help some people. Let me know if you have any questions.
Prague: we traveled by train from Berlin, when you book a train make sure to look at both Czech railways and DBahn. Czech railway ended up being almost half the cost. It was nice train ride and took about 4 1/2 hours. We had 2 full days in Prague so it was a packed 2 full days but very enjoyable. We stayed at Hotel Hastal, which was a great hotel with breakfast, AC, in a great location, and quiet. We went on a tour with Personal Prague Guides with Lenka. This was a great investment because she brought life to all the sites and easily got us around the city. We also learned a lot about the culture and the history of Czech Republic. That night we went on the Urban Adventures beer and tapas tour. We were actually surprised at how good the tour was! Our tour guide Travis has experience with brewing and brought us to a couple small bars with very good local beers, it was definitely one of the highlights of our trip. He also explained to us the history and culture of Czech Republic as well. We personally liked Czech pilsner/pale lager beers more than German beers. Day 2 in Prague we explored what we didn't see with our guide. One great off the beaten path cafe the tour guide recommended to us was Kavarna Novy Svet. It was on a beautiful side street, I think my wife probably took about 100 pictures of the street. We then went to a small microbrewery called Pivovar U Dobrenskych, which was recommend by our beer tour guide. They had very good beer/homemade food. We were also astonished with how cheap it was. For an appetizer, 5 beers, 2 entrees, 1 dessert and tip it was 45 euros!
Prague is an amazing city, I would definitely recommend more time & wish we spent more time there to be able to enjoy it more!