If you are there during winter, consider really warm slippers. Temples, shrines and castles are generally unheated. Japanese are very big on gift-giving. If you are someone's guest, they may give you a gift as well. It is good to be prepared with gifts for anyone you may visit or who may do you favors.
Small gifts are appropriate in many circumstances.
Small, light and unbreakable of course makes a lot of sense when you travel. However, if you need to give substantive gifts, the Japanese are extremely name brand conscious. Scotch and whiskey are much appreciated, as they are very expensive there, but go for the big brands. However, you face them when you use them. In remote areas, the facilities can be pretty unisex.