For the stuff you want to see in Krakow, you could actually see it all in just one day - the city is quite compact. Definitely two days is recommended, though, and the trip out of the city is a must.
I didn't like Vienna because it seemed to be too pristine and prettied-up for tourists. The tourist numbers and the high prices were overwhelming when I was there and I felt like I'd come to a theme park. Each to his own, of course.
Remember that if you are planning to take night trains - which are excellent - they are far more likely to be full on Friday and Sunday nights. (That is, if they fit with working hours - people often go to another city for the weekend.) Most of them need to be booked in advance in summer anyhow but you'll have better luck finding a place mid-week if you want to change tickets.
Thanks @maenad for the advice on the sleeper train, will take note and likely travel during mid-week.
Regarding Vienna, we are thinking of setting a base for a day trip to Bratislava and Salzburg/hallstatt. I will check out the price for accommodation and if it's too costly, we may change our plan.
We are planning for all these places though: :D. Hopefully 3 days is enough.
-Belvedere Palace
-Schönbrunn Palace
-Vienna Old Town
-Mozarthaus Vienna
-The Glitzy Krapfenwald Pool
-MuseumsQuartier
-UNO-City
-View From the 57 Lounge And Restaurant
-The Sacher Cafe
-Ringstrasse
-Café Central located at Herrengasse 14 in the first district of Vienna
-Spanish Riding School