You need to make an itinerary for what you want, and only you know what you like best.
Japan has many different aspects - its many temples/shrines, castles, shopping, arts, museums, gardens, hot springs, hiking, folk crafts, festivals, nature, pop culture, cuisine and so on.
So what interests you?
You can certainly browse some comprehensive info like on the JNTO Page, Japan Guide, official city websites with their own tourist guides, and Tokyo Cheapo. Osaka is more or less a clone of Tokyo, and you can skip a lot there during the day. The crown jewels in the region are Kyoto and Nara, plus Himeji with Japan's finest original castle. If there is any sight that is a must, it would be the Todaiji Great Buddha in Nara - absolutely stunning. For the rest, use the links above and do your research.