I had breifly considered doing this as I've been out here studying in the Tokyo Metropolitan area for nearly a year now. I'm no expert, I already know from other threads that there are people far more knowledgable then myself in these matters but I can try and give you a few things that could help out with your game.
There is a lot of 'holy ground' around Tokyo, there are a huge number of shrines and temples all of which have their own god/spirit/deity. There are spirits for entire reigons of Japan or one specific natural feature (mountains, lakes etc). Wikipedia or god-checker are good places to read up on the inter-relationships between these.
Japanese folk-lore has a long history of animals that can turn into people, often beautiful women, so shapeshifters might be a good avenue of exploration. I have an NPC that is a fox-spirit of knowledge, called a Kitsune. I can send you what I have on that if you think it would be of help.
The Japanese element system is different to the greek one standard Dresden uses- there are already qualities assinged to each element so building a new element set for wizards should be pretty easy and give your games a nice eastern flavour. The same applies to the Yin-Yang which myself and one of my players recently built a set of elements out of. Again if either of these would be helpful I can send what I have across.
Some traditional martial arts- Kendo, Iaido, Kyudo, Judo etc are still frequently practiced by people of all ages all over the city. As such its not uncommon to see people carrying equipment around for this with them on the subway system and in the city- having a brief description of these and perhaps a few stunts might make a really appealing character for your players. As an example one of my teachers practices both Kendo and Iaido and often brings swords and armor into university with him on the subway. Truth be told he was actually very good inspiriation for another npc as he is also a devout Muslim and speaks three of four languages. Sometimes truth is a little stranger then fiction I guess.
Many people carry charms, Omamori, from temples that protect or help with a variety of things- everything from passing exams to safety when crossing the road. Perhaps the written prayers some of these items contain come from a true believer and hold a strong measure of power?
That being said, in my experiance talking with my Japanese friends, many go to various temples for festivals and things because its simply what you do rather then any very strong beleif in it. Perhaps this says more about the group of Japanese people I got to know or the younger generation in general rather then than the community as a whole but I would advise against making true beleivers very common in your npcs.
I hope some of this was some help.
