I organized a shuttle with shuttle lobo to take me from Vienna to my hostel in Český Krumlov for 1100 CZK or $60 CAD. When I factored in a train to Linz and then further transport, there wasn't much of a cost difference and the shuttle would save be a lot of hassle. However, there were some complications (I assume not enough people were signed up for the shuttle) and I ended up having to take the train to Linz anyway and had them pick me up at the train station. It worked out just fine in the end.
I started my visit with a visit the castle and the gardens. As usual, the best views are always at the top of the hill so be ready to do a little walking. Aside from visiting the castle there isn't too much else to do but wander through the narrow cobble stone streets and soak up the atmosphere, which can be tough to do mid-afternoon when the town is flooded with tourists. I preferred Český Krumlov in the morning and then again in the evening when there were fewer people milling about. That's when you can really hear the babbling of the water and if you time it just right, you'll probably get treated to some live music too.
The next day I boarded the Student Agency bus to Prague for 8 Euros. It was a great ride with comfy seats and personal TV screens. What a deal!