We are traveling in Sept from Passau to Prague and will have time for a 3 hour stop over somewhere on the journey to do a little sightseeing and grab a beer / glass of wine. We will already have visited Cesky Krumlow on our Viking river cruise earlier, so looking for another city / village to do a little sight seeing.
You'll love Tabor, halfway between Ceske Budejovice and Prague: historical town, beautiful market square, and small enough to explore most of it in the few hours you have at your disposal.
I second a vote for Tábor. Their Hussite Museum is really excellent, and the Goldie restaurant on the main square is well worth a visit.
I like Tabor too, there is an underground tour you can do from the Hussite museum ,there is also a nice little tower and medieval museum there too,actually plenty for a day trip never mind a 3 hour stop over.