With the recent addition of Google street Maps in Japan, here are a few of the earliest known Google Maps mashups that exist:
I'm not sure if this is a mashup, or just a local search result from Google Maps for Japan but Tokyoartbeat.com has venue information data on all of the galleries and museums in Tokyo so you can now see that data within Google Maps.
Also, here is another mashup (thanks nagoyan the earthhopper!) displaying filming locations of Japanese television shows. Based on an existing database, you can search by your favorite TV drama title and town. (Keep in mind that this app is mostly in Japanese - there are some English labels)
If anyone finds any other Japan Google Maps mashups, please feel free to post them in the comments section!