I think 3 days is enough to do Prague in. We were there for two which wasn't quite enough - the Jewish Museum is excellent and is half a day on its own. You could do a daytrip from Prague to Dresden, the train journey along the bank of the Elbe is beautiful. If you can get a direct train it takes just over two hours.

There are a lot of nice cities in Holland and it's a an easy country to get around by rail. IIRC Groningen and Nijmegen are very nice (I spent about a fortnight travelling round Holland a few years ago and it's all started to blend into one).