Aeronautical Charts used to be produced by NOAA (National Oceanic and Atmospheric Administration). That job now belongs to the FAA under their National Aeronautical Charting Office.
The yellow depicted areas on the sectionals are Category 1 and 2 Large Cities and Towns as defined by the NOAA according to population density. By the NOAA definitions these would be considered congested areas. One of the criteria I believe is that to be Category 1 or 2 the area must be an incorporated city or township therefore most rural areas would not qualify even though the population density may be quite high in some areas.
By FAA definition a congested area is any open air assembly of persons or dwelling and doesnt depend on population density or incorporation status of the area. The FAA definition is based on interpretations of the AIM, Part 91 and Part 137 (Agricultural Ops) and is not set forth in Part 1 which is why its a good idea to check with the local FSDO regarding their interpretation
One is a cartographer's definition and the other the regulatory definition. As a pilot one would probably want to stick with the regulatory definition of congested airspace.
NOAA used to publish a 40 or so page guide that explains all the details of a sectional chart including the yellow areas but I dont know where it could be obtained these days. Maybe from the new FAA NACO.