Kyoto is a uniquely spectacular place for foliage peeping during fall. The city, capital of Japan for more than thousand years, has hundreds of temples and shrines spread across the city and its forested, mountainous outskirts. Many of these places feature gardens that are carefully maintained (see my favs on Google Maps).
Of course, autumn colors vary in intensity and progress each year. Well, if you go in the second half of November, you should see some crimson-colored maple leaves (momiji) for sure. A great resource for planning an itinerary are the autumn color reports from japan-guide.com.
In many ways, Kyoto seems like a reverse image of the incomparably larger Tokyo. It has a distinct little-town feel, contrasting its size and population, almost 1.5 million, after all. More than a dozen of its temples, shrines and other monuments are acknowledged as UNESCO World Heritage Sites. In order to preserve these historic landscapes, the city has put strict building regulations in place, preserving its prevailing low-rise skyline.