Both countries are famed for their beer. I would suggest combining chess and beer like this: 
On a more serious note, Game & Puzzles Wenceslas Square 38 New Town, Prague 1 Czech Republic sells chess related things. Think some czech Gms run a bookstore somewhere but don't know the address. Also, the Czech republic has awesome glass chess sets at souvenir places.
Thanks for the advice.
That's my question! Can you give me a couple of chess stores in Prague and Berlin, because I'm going on a trip with my friends and I would like to know where I can find some chess related stuff! Cheers!