Praha to Krakow

A few years ago, I found the overnight train to be perfectly fine, not much different from most, not the newest or fanciest. There should no longer be any need to wake you up for a border check, since both countries are now in the Schengen visa agreement. I booked a bunk in a triple and was lucky to get the compartment to myself. Sleepers are cheaper than on this route than they are further west. At the same time, I'm not bothered by an 8-hour daytime train ride with one connection. That just becomes the plan for the day (hopefully with a book and lunch in hand).

Have not visited Olomouc. A morning departure could get you there in 2.5 hours, leaving a generous half-day for sightseeing.

We did our last overnight trains a LONG time ago. We had the same concerns except that we traveled from Krakow to Prague. We chose to overnight in Olomouc and and it was very nice. Each train journey is about 4 hours as I recall. We arrived in the early afternoon and left in the early afternoon the next day. It was quite easy to tram or bus from the station to the main square where we had a room reserved and back the next day to resume our trip to Prague. Olomouc was very pretty, and we felt we did OK with the short time we spent. We walked all around, saw several sights, and just sort of took it easy as the main purpose was to avoid an overnight train ride. No regrets. CK is beautiful, rather small, but I have no idea how one would travel from there on to Krakow. We spent 3 nights in CK in May, and had a great time, canoed the Vltava one afternoon--that was a lot of fun. Easy paddle, BBQ and beer stop about halfway, and return transport to canoe livery in CK. Our itinerary took us from CK to Salzburg. As I recall, after leaving Krakow we changed trains in Katowice, Poland and that was easy as well. Good luck and safe travels.

Overnight train is the only direct train. Not good for light sleepers. Many stops and connecting and disconnecting carriages in Bohumin. Otherwise there is at least one change in Katowice. Another option is by shuttle bus, check:
http://www.tigerexpress.eu/en/
I like the idea to stop in Olomouc. Olomouc is like a little Prague without crowds. It used to be the capital of Moravia. Now it is Brno. Moravia is eastern part of the Czech Rep., Bohemia western part. You can get to Olomouc from Prague by Supercity Pendolino train in 2 h 14 min. The fastest connection from Olomouc to Krakow is by Supercity Pendolino to Ostrava hl.n. (hlavni nadrazi - Main Train Station) and from there by bus to Krakow. It all takes 3 h 44 min. You will have half an hour time in Ostrava. You can check Deutsche Bahn website for more options. You can find more information about Olomouc in Rick Steves guidebook Prague & the Czech Republic.

I spent an overnight in Olomouc in 2007 (going to and from Prague), and it was delightful. The central fountains and Europe's largest Plague Tower are certainly worth seeing; Rick's Prague And The Czech Republic book has a very good chapter with other highlights. At least in 2007, I felt like I was one of the few visitors.

Cesky Krumlov is also very interesting, but much more visited, and far out of your way from Prague to Krakow.

I rented a car in Prague, drove to Krakow, then drove to CK and back to the airport in Prague to return the car.... it was really easy, a beautiful drive and did not take nearly as long as the train. Stopped at Kunta Hora, Auschwitz and a few fun little towns along the way.