I did a 6week trip of Europe the year before last and we managed to squeeze in Bratislava, Budapest, Krakow and Prague.
Bratislava is a lovely place but really small with not much to visit, so i would leave that out. Ive heard Vienna is a great place to visit if you get the chance. I would definatly recommend to go to Budapest, its a very cool city, with great history and loads to explore.
If your thinking of going up to Krakow, i would recommend to visit Auschwitz, it isnt a pleasant place, but a great experience.
Prague is a fantastic city, with so much history, we went on a great day tour as we wanted to learn about the history and didnt have long. The tour opperator we used met on the main street, we met some great people on the trip as well.
Hope that helped, Have a great trip
Emma