First tell us why you are going to Japan, i.e. what you are interested in. Some people want to spend most of their time in Akihabara, Disneyland and Sanrio Puroland, others want to see castles, shrines and temples, and some want to stay away from the cities and go hiking in the Japan Alps and Shiretoko Pensinsula for example.
How long are you staying?
Have you looked at sites like
japan-guide.com - Japan Travel and Living Guide Lots of recommendations there.