Historic, beautiful and easy to get around
Prague is a stunning place to visit for it's architecture and history. Our self-catering apartment was a five minute walk from the square and then on a little to other tourist attractions. The train station was five minutes too. Nothing posh or fancy but very clean and comfortable and we could cook. It is called Salvator Superior Apartments. A supermarket for food and wine was across the road as was a great salad place.
From Prague we took the bus out to Cesky Krumlov. One to put on your list but go early morning. Take a look at the photos in the link by clicking on the Cesky Krumlov link above.