We have 3 nights in Vienna and 5 nights in Prague. I'm thinking of taking the overnight train to Chesky Krumlov, spending the night there and then continuing on to Prague. It doesn't seem practical to do Chesky Krumlov as a day trip out of Prague considering the bus takes 3.5 hours.
IMO, 5 nights in Prague is too much time, although others may disagree. As you've been considering, I think you'd be well-served to consider another stop between Vienna and Prague for 2 nights.
I haven't been to Cesky Krumlov (and was not aware there was an overnight train between Vienna and CK?), but it's in the Rick Steves guidebook and many people on this site have visited and seemed to have enjoyed their stays. Another place I'd enthusiastically encourage you to research as a possible stop is Brno, which is located on the main train line between Vienna and Prague. It's the second largest city in Czech Republic and gets very little tourist traffic, which doesn't make a whole lot of sense to me because it is rich in history and filled with interesting sights. PM me if you'd like more information.
I would agree that 5 nights in Prague seems like a bit much, though I guess it depends on your day trips. When we visited Prague, rented a car and spent 4 nights in the countryside. Two nights in Telc and two nights in Olomouc. We liked both, but especially Telc. There are a number of very interesting old castles in the area to visit. You could rent a car from Prague and visit Cesky Krumlov, or Telc, or wherever. Or you could rent a car from Vienna and drive to Prague, stopping wherever you like on the way.
5 nights in Czech Republic is not too long...you can stay in Prague 4 of the 5 nights and do the over nighter in Cesky Krumlov. Student Agency Bus is a good option at 13 Euro round trip per person it's a good deal. And the bus ride is only 2.45-3 hrs depending on what time you go. There's one that leaves a few long blocks away from Andel Metro at 7am that arrives 9:50am at Cesky Krumlov. There are two stops in CK....one a short hike from town center and the other a short hike from the Castle. Make sure to pick the stop best suited to your needs. Here's the website: http://www.studentagency.cz/
I'll have to take the opposite stance and say that five days in Prague sounds perfect to me. It's one of those cities -- if you love it, there's never enough time. Your plan sounds spot-on, at least to me. Have fun!
Shelley...Prague is a great visit - it is a place that is very scenic and it attracts a very young goup of tourists. I agree with those above that feel five nights in Prague is more than you need. I would use two nights somewhere else.