Yakutat displaced Sitka, Alaska, which displaced Juneau, Alaska as the largest city. Sitka is 2874 square miles and Juneau is 2717 square miles (Sitka was the earliest large city, having been formed through incorporation of the borough and city in 1970).
Yakutat is a perfect example of an "overbounded" city, which refers to a city that has boundaries that extend far beyond its developed area (certainly the glaciers and ice fields in the city won't be developed soon.)
Jacksonville, Florida is the largest city in area in the contiguous 48 states at 758 square miles. Jacksonville includes all of Duval County, Florida with the exception of the beach communities (Atlantic Beach, Neptune Beach and Jacksonville Beach) and Baldwin.