Central European cities - bakery recommendations?

We're following the college daughter to her summer nanotech program (okay, yes, I'm proud), and adding on a trip. While my family is out hiking or drinking world-famous beer, I hope to be tasting the delights of bread in these cities: Berlin, Munich, Budapest, and Prague. I'm especially interested in what I think is the specialty of the region, rye breads. The only glitch is that I do not know of any bakeries there.

Any recommendations would be greatly appreciated. I'm hoping for a transcendent and inspiring bread journey.