Where to stay between Budapest and Krakow?

I wouldn't stay in Breclav or Ostrava. Breclav is just a small town with an important railroad crossings. Ostrava - big sprawling city with steelworks and mining industry. I would get off your train between Breclav and Ostrava in Prerov. From there in about 20 minutes by train you get to Olomouc. Nice historical city, see Rick Steves: Prague and the Czech Republic. From Olomouc there is a direct train to Krakow. The shortest way is through Slovakia. But that would have to be done by car or bus. In that case I would stay in High Tatras. Almost the whole ride through Slovakia is very scenic. Especially Low Tatras (but they are not low) and High Tatras. These peaks are looking from the south you would be approaching even higher than they really are.

My guess is that there is no optimum place to spend the night between Budapest and Krakow. I remember nothing but small villages.

We drove it by auto in 1998 and stopped at a B&B in a small town or the border in the mountains recommended to us by friends in Krakow.

If I were making your decision, I would choose to take the overnight train and sleep on it.

Which site did you go to check the rail? The site I'm using is
http://plannerint.b-rail.be/bin/query.exe/en?ld=IA&L=profi&OK#focus

It lists several Olomouc's. For example and I'm still trying to figure this out when checking the rail info. Olomouc hl.n. or Olomouc mesto or Olomous-Repcin, etc.
Thanks for the suggestion! Now I need to figure out the rail and what the listing after the city name mean. Anyone know where I can find this information?

I am using Deutschebahn website. I get to it through Rick Steves website. All the listings under Olomouc are just for one Olomouc. Those are different stations in Olomouc. You get off at Olomouc hl.n. (hlavni nadrazi) which means main railroad station.

Going by car is a totally different route than going by train as I already mentioned. There is only one direct train from Budapest to Krakow. Leaving B. at 19:58 arriving to K. at 06:33. It's a sleeper. If you want to stop in Olomouc the best seems to depart Budapest Keleti pu at 9:28, it arrives in Breclav at 12:54, there you change to another train departing from Breclav at 13:28, arriving to Olomouc at 14:52. From Olomouc there are two direct trains to Krakow. First 16:54 arriving to Krakow at 21:46 (I would go for this one) and then train leaving 3 minutes after midnight and arriving to Krakow at 06:33.

I did see that the night train is a direct one from Budapest to Krakow. It will be me and my daughter 16 yrs. My concerns for the night train are is it safe with a clueless 16 yr. old? What about using the bathroom in the middle of the night? Is this a concern? Seems like silly concerns but I have found I need to be one step ahead when we are traveling alone.
Thanks again for all the suggestions! I will check out the German site listed here.
Laura

My wife and I took the sleeper from Krakow to Budapest. We had the room to ourselves and felt safe. It locked from the inside and we got woken-up 3 times to show our passports and really only got about 3 or four hours sleep, but it was nice anyway. Each car had a WC and it and the room were very clean. The porter was nice and gave us coffee and a croissant in the morning. My wife left the room a couple times on her own and never felt unsafe. You can see pictures of are trip at:

http://gadtravel.blogspot.com/

Eger is worth a overnight, but agree that it would be best to spend more time in Krakow and Budapest.

Well, now nobody will be waking you up to check your passports. It's all schengen zone. Direct train Budapest to Krakow no more goes direction Eger but Bratislava, Breclav, Ostrava.