Naturally, I can only comment on those I have personally visited. To do otherwise would obviously be inappropriate.
Favourite is fairly easy: Edinburgh, UK, narrowly beats Munich, Germany. The two cities are incredibly beautiful and atmospheric but Edinburgh just sneaks it for its truly incomparable ambience.
Least favourite of those I have visited is a toss up between Brussels, Belgium and Budjevice, Czech Republic. Found Brussels to be filthy and Budjevice to be what anyone from the West would earmark as a drab, Communist era stereotype. In the latter instance, this is a shame, as most of the other cities in the Czech Republic are truly beautiful.