I'll give it a try..

I'll bring this selection over to the main summary page at http://www.worldheritagesite.org/allbyrank.php :

Amsterdam - for its architecture and historical importance
Ubeda/Baeza
Bordeaux
Budapest - contrast across the 2 sides of the river, great location and the 19C "modernity
Christiansfeld
Luxembourg City
Weimar
Dubrovnik - rather fine in its architecture and location
Florence - Renaissance town par exellance
Brussels - Grand Place -
Guimaraes
Holasovice
Holloko
Ibiza
Kutna Hora
La Chaux-de-Fonds/Le Locle
Mostar - mostly for its bridge
Nancy
Berne
Rauma
Paris - iconic. Important for town planning
Röros
Riga - for its Art Nouveau parts
San Marino
Hamburg
St. Petersburg - an excellent example of 18th century architecture and as a representation (together with Moscow) of one of the largest empires in the world.
Trebic
Urbino
Val di Noto - Excellent representation of the Baroque era
Valletta
Vicenza
Vienna - For its 19th century Ring
Vilnius
Vlkolinec (better under rural)
Yaroslavl
Zamosc