I am actually attending a conference in Japan this summer and already have a specific target in mind for research: A comparative study of the effects of women participation in the workforce.
In my Econ of Japan class, we spent a significant amount of time discussing the economic implications of women working, I decided for my research to focus on the social implications.
After browsing through the websites, I found J-stor to be most helpful, however sometimes its articles are not very recent.
The website from Indiana university East Asian Studies center seems to give alot of useful links but I havent gone through them.
Also the East Asian library from UCLA also provides alot of links and resources.
The Electronic journal of contemporary japanese studies has some interesting articles, but it does have many. Worth making a search to see if your topic of interest can be found there.
I liked Asia times as it had different articles on current issues, from different viewpoints.
Many of the websites can help one find an interest, but does not exactly help in detailed research resources (some require you to pay)