Belize City is the former capital of Belize, and I suppose San Salvador can be also included with this list.
Guatemala comes from the Náhuatl word Quauhtemallan, meaning land of many trees. Like Mexico, the city was founded/claimed first and the name was extended to the rest of the territory later. El Salvador was the province of San Salvador (named after the settlement) before its first constitution in 1824. It then merged with another territory called Sonsonante and became the state of Salvador (Estado de Salvador). The name eventually became El Salvador in the 20th century.