Kamakura, in Kanagawa Prefecture, was once the capital of Japan and is a short day trip Tokyo. Kamakura offers a very nice change of pace if you feel like you need to escape the busy streets of Tokyo. Kamakura is perhaps most famous for the Big Buddha, 2nd largest in Japan, but also has other famous temples and shrines such as Engakuji and Hachimangu.
Nara is in the Kansai Region of Japan and is about 30-40 minutes by train from Kyoto or Osaka. Nara, the old capital of Japan, is home to 8 of Japan’s UNESCO World Heritage Sites and 64 of the 200 and some odd buildings that are considered national treasures in Japan. Nara is also home to about 1200 or so deer that roam freely around Nara Koen (Nara Park). I have been to Kyoto more than 5 times but just recently went to Nara for the first time because I thought it would feel similar to Kyoto; however, it has a very different feel from it. Partly because there are deer running around everywhere and partly because it is less crowded (although the famous spots like Todaiji, do get very crowded at times), but there is something about Nara, that is somewhat hard to pinpoint, that makes it a magical place.
I highly recommend checking Nara out, especially in the fall. If you want, you could probably see most of Nara without staying overnight, but I recommend staying one night there just to make sure you can see everythign you want to see. Below are a few places that you will not want to miss: