Before you begin your research, you might want to check the following points for basics:
JapanKnowledge: What is the general understanding of the topic of your research? JapanKnowledge provides access to basic Japanese reference sources including encyclopedias and dictionaries (e.g., 日本大百科全書, 日本国語大辞典, 國史大辭典, Encyclopedia of Japan, etc.) as well as 東洋文庫 and 新編日本古典文学全集 series. JKBooks includes Taiyō 太陽 (1895-1928), Bungei kurabu 文芸倶楽部 (1895-1912), Fūzoku Gahō 風俗画報 (1889-1916), Tōyō Keizai Shinpō 東洋経済新報 (1895-1945), The Oriental Economist (1934-1985), Bijutsu Shinpō 美術新報 (1902-1920), and Takita Choin kyūzō Kindai sakka genkōshu 滝田樗陰旧蔵近代作家原稿集.
Risāchi nabi リサーチ・ナビ: Are there useful research guides for specific topics or specific types of materials? The National Diet Library of Japan provides many research guides covering a wide range of subjects and special materials.
Kaken: What kind of research has been done on the topic of your research? Kaken is a database of Grants-in-Aid for Scientific Research, providing the latest information of the research projects and reports in Japan. The database is provided by the National Institute of Informatics (NII) with support of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and the Japan Society for the Promotion of Science (JSPS).
Whoplus: Contains biographical information of 330,000 prominent figures active in Japan and e-version of several biographical reference dictionaries covering 280,000 people, including Jinbutsu refarensu jiten 人物レファレンス事典, Umi o koeta Nihon jinmei jiten 海を越えた日本人名事典, Jitenkindai Nihon no senkusha 事典近代日本の先駆者, Tsuitō kiji sakuin 追悼記事索引1991-2005, Bijutsu sakuhin refarensu jiten: jinbutsu, shōzōga hen 美術作品レファレンス事典:人物・肖像篇, Shashin refarensu jiten: jinbutsu, shōzōga hen 写真レファレンス事典人物・肖像篇. Because "Who" database is charged by usage, please click the name entry or "経歴情報" link only once when needed.
Directory of Japanese Studies in the United States and Canada: This website displays the information collected from the Survey of Japan Specialists and Japanese Studies Institutions in North America in 2011-2012 sponsored by the Japan Foundation.The survey was conducted through the University of Hawaii under the direction of Professor Patricia Steinhoff of the University of Hawaii and Professor Julian Dierkes of the University of British Columbia.
J-Global: Who does the research in the academia and what research resources are available in Japan on your topic? J-Global maintained by the Japan Science and Technology Agency provides information on research institutes, researchers, research projects, etc.
Academic Society Home Village: What academic societies exist in a specific field? The National Institute of Informatics compiles links to homepages of academic societies in Japan.
JapanGov: The Japanese government's official website.
Portals to Archives of Web Sites and Databases
Here is a short list of useful resources for navigating through archives of web sites and databases--often not searchable with major search engines:
Dai Kan-Wa jiten 大漢和辞典 / 諸橋轍次著: The most comprehensive dictionary of Chinese characters from Japan (ca. 50,000 characters with ca. 500,000 word entries). 語彙索引 in Japanese alphabetical order is also available.
Nihon kokugo daijiten (dai 2-han) 日本国語大辞典 (第2版): The most comprehensive dictionary of Japanese language (ca. 500,000 entries). Provides meanings, usages in old literary or historical works, variations of words in dialects, etc. A more updated online version of the dictionary is available via JapanKnowledge.
Rikai: Program for learning Japanese, which also provides readings and definitions of Chinese characters in English; created by Todd David Rudick utilizing the resources made available by Jim Breen and his EDICT Project.
Weblio: Supports translation from Japanese to other languages.
Japanese Historical Language Dictionaries
Here is a short list of Japanese historical dictionaries and guides to them:
Whoplus: Contains biographical information of 330,000 prominent figures active in Japan and e-version of several biographical reference dictionaries covering 280,000 people, including Jinbutsu refarensu jiten 人物レファレンス事典, Umi o koeta Nihon jinmei jiten 海を越えた日本人名事典, Jitenkindai Nihon no senkusha 事典近代日本の先駆者, Tsuitō kiji sakuin 追悼記事索引1991-2005, Bijutsu sakuhin refarensu jiten: jinbutsu, shōzōga hen 美術作品レファレンス事典:人物・肖像篇, Shashin refarensu jiten: jinbutsu, shōzōga hen 写真レファレンス事典人物・肖像篇.
JapanKnowledge: In addition to basic Japanese reference sources including encyclopedias and dictionaries (e.g., 日本大百科全書, 日本国語大辞典, 國史大辭典, Encyclopedia of Japan, etc.), JapanKnowledge provides access to 東洋文庫 (平凡社) and 新編日本古典文学全集(小学館) series.
Japanese Text Initiative = 日本語テキストイニシアチブ: Texts of classical and modern literature; collaborative effort of the University of Virginia Library Electronic Text Center and the University of Pittsburgh East Asian Library.
Social Science Japan Data Archive (SSJDA): Archive of social science data concerning Japan. The SSJDA collects, compiles, and digitizes micro-level data on Japanese society, and offers them for secondary analysis.
Reference managers (also called citation managers or bibliographic management software) offer a way to save, organize and manage references. Many work with word processing software to format in-text citations and bibliographies for papers and theses, allow you to share references, and enable you to attach or link PDFs to a citation record.