1. Nihon rekishi daijiten, 日本歴史大辞典 by Kawade Shobō (revised edition, 1968-70) The most useful historical encyclopedia. Twelve volumes, Indexed.
2. Sekai rekishi jiten, 世界歴史事典. by Heibonsha. 25 vols. (1951-55) Very good on general topics; Indexed.
3. Kokushi daijiten, 國史大辭典 by Yoshikawa Kobunkan (1979-98 ) A superior historical encyclopedia.
4. (Kadokawa) Nihonshi jiten, 角川日本史辞典 edited by Asao Naohiro, Uno Shunichi, and Tanaka Migaku (1996) A small but reliable historical dictionary. (Botsman’s top choice!)
5. Nihon shi jiten, 日本史辞典 (revised edition, 1962) and Nihon kindaishi jiten 日本近代史辞典 Good for quick reference and full of innumerable tables containing all sorts of useful information. Compiled by Kyoto Daigaku Bungakubu Kokushi Kenkyūshitsu.
6. Nihon kingendaishi jiten, 日本近現代史辞典 (1978) (RJ 3380/6531) A good recent dictionary of the modern period.
7. Nihon keizaishi jiten, 日本經濟史辭典 (SJ 4153.5/6523) Especially good for the Tokugawa period. Kanji index.
8. Nihon gaikōshi jiten, 日本外交史辞典 (1979) (RJ 3317.7/2192) Compiled by Gaimushō Gaikō Shiryōkan
9. Nihonshi daijiten, 日本史大事典 7 v. Heibonsha, 1992-4. An important recent encyclopedia.
10 Nihon rekishi taikei, 日本歴史大系 6 v. Inoue Mitsusada... [et al.] hen. Yamakawa Shuppansha, 1984-89
11 Shinpan Nihon shi jiten, 新編日本史辞典 Kyōdai Nihonshi Jiten Hensankai hen. Sōgensha, Heisei 2 [1990]
12 Nihon kindaishi jiten, 日本近代史辞典 Kyoto Daigaku Bungakubu Kokushi kenkyūshitsu. Tōyō keizai shinpōsha, 1958.
13 Shinpan Nihonshi Jiten, (Kadokawa, 1996)
Asian Historical Encyclopedias
These are useful works for quickly tracking down the references to Chinese and Korean history and thought that are numerous in pre-modern and early modern Japanese writings.
13 Tōyōshi jiten, 東洋史辞典 (revised edition, 1967) One-volume Kyoto University encyclopedia that parallels 3.d.
14 Ajia rekishi jiten, アジア歴史事典 by Heibonsha, 10 vols. (1959-62)
15 Tōyō rekishi daijiten, 東洋歷史大辭典 by Heibonsha, 9 vols. (1937-39)
Other Encyclopedias
17 Sekai dai hyakka jiten, 世界大百科事典 by Heibonsha, 32 vols. (1955-59, plus later supplements) A comprehensive encyclopedia useful for general purposes; but also for a variety of other uses. Consider for example the article on suicide or the article on divorce with their comparative material on the social history of modernization.
18 Dainihon hyakka jiten (Encyclopedia Japonica), 大日本百科事典 by Shōgakukan, 23 vols. (1967-72)
19 Nihon bungaku daijiten, 日本文学大辞典 edited by Fujimura Tsukuru, 8 vols. Useful for literature, with information on authors, plots of novels and plays, etc.