If limited on time, you can get a feel for most places in a quick day or two. However, I would add Krakow to the list of cities where you need at least three days to feel like you saw a fraction of what you wanted to see. Others on that list include Washington DC, New York City, London, Paris and Berlin.
Day #1: Get your bearings by taking a free walking tour of the city. http://freewalkingtour.com/krakow/. After you have learned a bit about the history of the city, return to the Wawel Castle. In the afternoon, return to the market square to visit the underground museum, cloth hall, and St. Mary’s Basilica. There are also several cafes lining the square that are perfect place to people watch while enjoying a meal or a drink. Krakow also has some fantastic street food and I had some potato pancakes from a small kiosk that still visits me in my dreams!
Day #2: You can spend an entire day in Krakow Ghetto, Kazimierz. Do not miss Schindler’s factory and plan to spend a couple of hours in the former enamel factory. http://www.mhk.pl/oddzialy/fabryka-schindlera Spend the next several hours visiting the Jewish Museum, and old Synagogues. Make sure to plan time for lunch or dinner here as well.
Day #3/4: You need an extra day to get out of the city center and go to Auschwitz and / or the Wieliczka salt mines. As a note, I did not love the salt mines and would not recommend them. However, they are a UNESCO sight and most people love them. Both sights are easy and significantly cheaper to do on your own using the local bus rather than one of the many advertised tours from town (you will need to join a tour once you arrive).http://www.auschwitz.org/ and http://www.wieliczka-saltmine.com/
Books and Movies: Schindler’s List. The Kommandant’s Girl by Pam Jenoff.