This entirely depends on your interests! Japan has something for nearly anyone though. A lot also matters on where in Japan you are going and when.
No visit to Japan is really complete without a visit to a hot spring (onsen) - they are literally all across the country and can be very inexpensive to the wildly exorbitant at high priced Japanese inns (ryokan).
And since Japan is around 70% mountains, there is always some great hiking nearby.
Plus there are many festivals, almost always something happening someplace whenever you go. If you have a chance to see one, by all means go - it is a window straight into Japanese culture.
There are also some great traditional Japanese gardens and parks to visit - even in Tokyo. Costs are very low and some are free. And in the big cities there are some great skyscrapers to see some of the city, both day and night. There are pricey places like in Tokyo the Sky Tree and Roppongi Hills, but there are lots of free ones also.
For other ideas in the Tokyo area, try browsing Tokyo Cheapo.
It's up to you to do your research and make the most of your trip to Japan.
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