One of my favorites: Madison, Wisconsin.
Blue represents Lakes Mendota and Monona, the white stripe represents the isthmus between these two lakes, the black cross represents the four lakes of the area (Mendota, Monona, Wingra, and Waubesa) as well as the outline of the Capitol building, and then a Native sun a la New Mexico.
Not bad considering Wisconsin and some its flags *cough* Milwaukee *cough*