Here is the list of various places that have been recommended to us. For ease of use, I have divided it up into things to do in Tokyo, and places to visit elsewhere in Japan.
Here also is a Google layer I have been working on.
For what to eat and coffee to drink – we recommend getting the Foursquare app and following us – we have put together lists of where we have been/would like to go. As for coffee, check out this Cafemap for the best coffee in and around Tokyo as is voted on Instagram (updated daily).
Please leave any suggestions you have below! Feel free to be as general, or specific as you like.