All data is from 2010, unless otherwise noted. From the largest Central America city (in terms of metropolitan area population) on down:
Guatemala City, Guatemala
Metro area population: 2,945,080
City population: 1,104,890
Guatemala City is the capital of Guatemala, and the largest city in Central America. Its airport, La Aurora International is the fourth biggest in Central America in terms of passenger traffic. Crime is relatively high in Guatemala City compared to other Central America capital cities, but the city's proximity to Antigua, Lake Atitlan and other Guatemala attractions make it an ideal spot to fly into.
Metro area population: 2,408,000
City population: 2,201,000
Managua is the capital of Nicaragua, and the second-most populous city in Central America. It wasn't always the capital of Nicaragua – in earlier centuries, that title alternated between the Nicaraguan cities of León and Granada. Managua is relatively close to popular Nicaragua travel destinations like Granada (just 40 minutes away), San Juan del Sur and Ometepe.
San Salvador, El Salvador
Metro area population: 2,290,000
City population: 540,898
San Salvador is the capital of El Salvador. The metro area of San Salvador is the second largest in Central America, and includes the big cities of Soyapango, Apopa and Mejicanos, among others. San Salvador boasts some of the tallest high-rise buildings in Central America.
San Jose, Costa Rica
Metro area population: 1,707,620
City population: 347,281
San Jose is the capital of Costa Rica. While the city itself is big, the San Jose metropolitan area is home to a third of Costa Rican population. Most of San Jose is quite safe and traveler-friendly, and its location in Costa Rica's central valley makes it a great spot for travelers intent on exploring attractions in every direction. Juan Santamaría International Airport is the second-busiest in Central America.
Metro area population: 1,324,000
City population: 1,126,534
Tegucigalpa is the capital of Honduras. The city was founded by the Spanish in1578, but wasn't made Honduras's capital until 1880. Today, Tegucigalpa suffers infrastructure and poverty problems, especially in its sister city, Comayagüela. Crime is also on the rise in Tegucigalpa. Although central to certain Honduras attractions, many travelers opt to fly into San Pedro Sula instead.
Panama City, Panama
Metro area population: 1,272,672
City population: 880,691
Panama City is the capital of Panama. It's often considered the most cosmopolitan city in Central America, due to extensive American influence in the last century because of the Panama Canal. Panama City has the tallest high-rise buildings in Central America, expansive shopping malls, and many worthwhile attractions for travelers. Panama City's airport, Tocumen International, is Central America's busiest.
San Pedro Sula, Honduras
Metro area population: 802,598
City population: 538,101
San Pedro Sula is the second-largest city in Honduras, and home to the Ramon Villeda Morales International Airport. Founded in 1536, San Pedro Sula is considered Honduras's industrial center. Though very busy, it's more traveler-friendly than the Honduran capital city of Tegucigalpa.
Other large cities in Central America (that aren't included in a larger city's metropolitan area):
San Miguelito, Panama
City population: 293,745
Santa Ana, El Salvador
City population: 245,241
City population: 222,828
City population: 175,000
La Ceiba, Honduras
City population: 174,000