Keeping in mind that my trip was in 2005, I wouls have to agree that Tallin was the pick of the capitals. We used bus most of the time.
A suggestion for outside the capitals- I suggest that Tartu in Estonia is certainly worth a couple of days.
Keep in mind that some areas seem to be pretty seasonal. Our trip in late Sept meant that some spots were in shut down mode eg Curonian Spit. I also remember having to help push start the bus when we were leaving.