A list of largest cities with most recent data:
Reference 1: Population and Agglomeration.
Reference 2: Istanbul*, Bucharest, Sofia, Belgrade, Zagreb, Athens, Skopje, Tirana, Plovdiv, Varna, Thessaloniki, Cluj-Napoca, Timișoara, Iași, Constanța, Ljubljana, Novi Sad, Sarajevo, Craiova, Çorlu and Brașov.
Source: http://en.wikipedia.org/wiki/Balkans
Reference 2: Istanbul*, Bucharest, Sofia, Belgrade, Zagreb, Athens, Skopje, Tirana, Plovdiv, Varna, Thessaloniki, Cluj-Napoca, Timișoara, Iași, Constanța, Ljubljana, Novi Sad, Sarajevo, Craiova, Çorlu and Brașov.
Source: http://en.wikipedia.org/wiki/Balkans