During my times in Amsterdam i´ve found many nice things in Rush Hour (http://www.rushhour.nl
). It has mostly been different kind of world music, but they also have a small but fine selection of reggae vinyl - mostly reissues as i recall. I also heard that there exists a really nice shop out of the city center which should be the place to be if you´re looking for originals and rarities, but i´ve never visited that shop and never really found the exact location so correct me if am wrong, A-dam cats
Have a wonderful trip! Never been to Prague, but Amsterdam is a beautiful city, also in the winther time!