Like many of the European world heritage sites which encompass an entire city (Paris, Rome, etc) Kyoto is probably the grandest and most encompassing world heritage site in Japan.
Kyoto was specifically spared bombing in WWII by the allies because of its history. Unfortunately, many of the buildings did not survive the post-WWII modernization fervor in Japan.
Nonetheless, there is plenty to see in Kyoto and you can easily spend several days in the city viewing historic shrines and temples.