Which countries are commonly thought to be named after specific cities or towns? The city-states of Monaco, the Vatican City and Singapore are excluded as the city and the country are considered to be indistinguishable. Source
Not including hypotheses that are not generally accepted such as Guinea being derived from Djenné, Mali
Not including early settlements that are no longer in existence
Not including countries named after the word for a village, town or city in some language such as Canada
1. Not here because Oman is not named after Muscat. 2. Because the island of Sao Tome was given the name 'Sao Tome' first, and I assume the city was named after the island.