The climate in Tokyo is divided into four different seasons. You should pack your wardrobe depending on what season you are planning to vacation in Tokyo. Comfortable and warm shoes also a must-pack. Make sure that your socks do not have holes in them. Many homes and restaurants require you to take off your shoes before entering.
Plugs in Tokyo are the flat two pin type. If your electronic gadgets have the three pin, bring a converter plug.
Bring a deodorant. This commodity is not easy to come by in Tokyo. If you do find one, most likely, it does not work as good as the one you are used to.
Pack some over the counter medicines that you might need. Over the counter drugs in Tokyo are different from those at home. Also, bring a few extra prescription medicines that you might need.
Lastly, bring an English-Japanese dictionary. Not all people in Tokyo know how to speak English. To avoid the inconvenience of language barrier, it is always good to come prepared.