From all of those churches my favorite one would definitely be Our Lady of Ljeviš. It is an outstanding example of late byzantine architecture. Throughout its long history it was a holly place for Christians and Muslims, who converted it during the Ottoman rule and named Friday Mosque (al-jumʿa xhamia in Arabic). This name is still in use among Muslim Albanians in the city of Prizren.
Unfortunately the devastation of the paintings inside the church - initiated during Ottoman times - reached its peak during the march 2004 riots. The restoration of the site is still in progress.