My favorite stop in Europe was the Czech Republic, and my favorite stop in the Czech Republic was Prague. I fell in love with the city. So have a lot of other people, it is becoming a popular destination. Fortunately it isn't yet nearly as packed with tourists as cities like Paris, Rome, Vienna, etc. There is still time to visit before your impressions of crowds and lines will overwhelm your impressions of the architecture and people; I suggest getting there soon. But don't tell everyone about this; I don't want the whole world going to Prague.
After Prague I visited Cesky Krumlov. It is a pretty little town, and perhaps the most visited place in the Czech Republic outside of Prague.
Telc is a small town near the center of the Czech Republic that is a bit of a challenge to get to. My guide book said it is difficult to reach by rail, so I went there from Cesky Krumlov by bus. A little inconvenient, but not a great difficulty. The great thing is that this small inconvenience leaves Telc off the main tourist trails.
Brno wasn't highly recommended in my guidebook, but it was on my way to Vienna and an excuse to linger in the Czech Republic a little longer. I just hated to leave the country of beautiful women and great beer. I don't have much to show for my stop there, I created a separate page just for consistency.
That's if for the Czech Republic. I spent most of September there, more time than in any other country. And, more than any other country in Europe, I want to go back, for more time in Prague and more time exploring the rest of the country. Not because of the beer. Well, not just because of the beer; it is really a great place for a long visit. I understand why it is so popular with ex-pats.