Consulting some of these works is indispensable once you have settled on a topic, or are debating two or three possible issues for a paper.  They will point you to non-mainstream studies as well as those published in well-know journals.  Japanese scholars have prepared a truly extraordinary range of bibliographies over the years, ranging from comprehensive to extremely specialized.  There are also some helpful English language compilations of works in Japanese.

1.         Japanese Studies from Pre-History to 1990, A Bibliograhical Guide. 

Perren, Richard. Manchester University Press, 1992.

2.         Japanese history: a guide to Japanese reference and research materials.

Hall, John Whitney. University of Michigan Press, 1954. a)

3.         Japanese History: A Guide to Survey Histories. Part I By Period.

Fukuda, Naomi ed.  Ann Arbor: Center for Japanese Studies, University of Michigan, 1984

4.         Japanese History: A Guide to Survey Histories. Part II Literature.

Fukuda, Naomi ed.  Ann Arbor: Center for Japanese Studies, University of Michigan, 1986.

5.         Rekishigaku, kōkogaku ni kansuru 27-nenkan no zasshi bunken mokuroku: Shōwa 23-nen--Shōwa 49-nen. 歴史学・考古学に関する27年間の雑誌文献目錄　： 昭和23年～昭和49年

Nichigai Asoshietsu, Shōwa 57 [1982]

6.         Nihonshi ni kansuru 27 nenkan no zasshi bunken mokuroku.  Shōwa 23 nen - Shōwa 49 nen.  3 v.　日本史に関する２７年間の雑誌文献目録　：昭和２３年～昭和４９年

Nichigai Associates, 1982.

7.         Zasshi kiji sakuin, jinbun shakai hen, ruiseki sakuinban: 1970/74 雑誌記事索引, 人文社会編, 累積索引版.

Kokuritsu Kokkai Toshokan. Nichigai Associates, Kinokuniya Shoten, 1976. 

An extremely important and helpful source.

8.         Nihonshi tsūshi tosho mokuroku.　日本史通史図書目録．

Nichigai Asoshieetsu: Hatsubaimoto Kinokuniya Shoten, 1994.

9.         Nihon kodai chūseishi tosho mokuroku 日本古代中世史図書目錄

Nichigai Asoshieetsu: Hatsubaimoto Kinokuniya Shoten, 1993.

10.       Nihon kinseishi tosho mokuroku 日本近世史図書目錄

Nichigai Asoshieetsu: Hatsubaimoto Kinokuniya shoten, 1993

11.       Nihon kindaishi tosho mokuroku 日本近代史図書目錄

Nichigai Asoshieetsu: hatsubaimoto Kinokuniya Shoten, 1994.

12.       Kinsei kindai shiryō mokuroku sōran 近世・近代史料目錄総覽

Kokubungaku kenkyu shiryōkan, Shiryōkan eds. Sanseidō, 1992. 

Useful for identifying mokuroku for documents; arranged by prefecture and within prefectures by publisher

13.       Shiryō Nihon kin gendai shi. 3 vols. 史料日本近現代史

Sanseidō, 1985.

14.       Nihon keizai-shi dai-ichi (ni, san, yon, go, roku, shichi) bunken, seven volumes edited by Honjō Eijirō (1933-1977) 日本経済氏第一（二、三、四、五、六、七）文献．   

Don’t let the title to this work throw you off.  It is called keizai-shi only because Honjō was a professor at a keizai gakubu.  It contains annotated listings of books (and some articles) published in a great variety of fields, ranging from intellectual, religious, and political history to topics such as mining or forestry.  Vol. 1, research up to 1931; Vol. 2, 1932-40; Vol. 3, 1941-50; Vol. 4, 1951-57; Vol. 5, 1958-62; Vol. 6, 1963-67; Vol. 7, 1968-72.

The above are relatively comprehensive bibliographies, which cover an entire period or the entire sweep of Japanese history.  If you have a particular topic for which a specialized, l topical bibliography is available, by all means consult this first.  There are literally hundreds of these among the BJ numbers on the east wall of the Bibliography Room (off the main Reading Room) in the Harvard-Yenching Library.  To give a few examples at random:

Shintō ronbun sōmokuroku 神道論文總目錄　

Chihōshi bunken sōgō mokuroku 地方史文献総合目錄

Chōsen tōkei sōran　朝鮮統計総覧

Nihon gaikōshi kankei bunken mokuroku　日本外交史関係文献目録

Bakumatsu Meiji kenkyū zasshi mokuji shōran　幕末明治研究雑誌目次照覧

Hōseishi bunken mokuroku 法制史文献目錄

Nihon shakai shōgi bunken kaisetsu. 日本社会文献開設．Watanabe, Yoshimichi.  Otsuki shoten, 1958.

Bunken kenkyū: Nihon no rōdō mondai, (1975) 文献研究日本の労働問題

Also: Ishin shiseki kaidai (denki-hen) (1935). A description of biographical works and materials on figures of the Restoration period, and

Bunkakei bunken mokuroku, Vol. 14. Bibliography of biographies of figures from the Restoration to the modern period, including some Westerners who played a significant role in Japanese history.