Both are worth visiting, so you can't go wrong either way (I agree on the comment about there being too many places to see and too little time!!!).

They are very different cities, and Jacob has summarised the differences well. Krakow is definitely the less "touristy", though there are still plenty of tourists! I would anticipate a possible increase in visitors this summer due to the links between Krakow and Pope John Paul II.

Vienna is an impressive city, one of my favourite in Europe. Very easy to get around, impressive palaces, fantastic cafes.