Readable online
The sci.lang.japan FAQ section on Japanese names is a good general resource for both modern and historical naming practices.
Koop, A.J. and Inada, H. Japanese Names and How to Read Them: A Manual for Art Collectors and Students. London: The Eastern Press, Limited, 1923.
A vast dictionary of all types of proper names, listed by kanji, with an extremely useful section of explanations of how to read characters, numbers, and dates, how names are formed, what titles are used, etc. Fully searchable, although the word recognition is imperfect.
Gillis, I.V. and Pai P'ing Ch'i. Japanese Personal Names. Ann Arbor, Michigan: Edwards Brothers, Inc., 1943.
Mostly male names, listed by initial kanji. Although it was compiled in 1940, most of the names are suitable to the 18th and 19th centuries.
Denshi Jisho has a dataset of Japanese proper names that's simultaneously wonderful and horrific. Wonderful because it contains hundreds of thousands of entries, including obscure and obsolete kanji and marginal readings. Horrific because it seems to have accepted any name anyone threw at it, including weird one-off readings, names of video game characters, and transliterations of English names, and there's nothing to tell these entries apart from more typical entries. But if you do due diligence on the results, it's a great resource for finding and translating modern names.
Meiji Yasuda Life Insurance releases an annual ranking of baby names based on the names their members give to their newborns, and keeps records going back almost a century. It's highly unscientific (selection bias, anyone?) but as the only publicly released name list with any reliability, it's the ranking just about everyone uses.
Dictionary of Girls' Names | 女の子の名前辞書
Japanese-Style Female Names | 日本人のような名前 女性版
Kirk, LauraLynn. "Collective memory of Japanese naming rituals through the incorporation of anime and manga." Honors student thesis, Florida Atlantic University, 2008.
Komori, Yuri. "Trends in Japanese First Names in the Twentieth Century: A Comparative Study." Asian Cultural Studies. 28: 67-82. 2002.
Nomoto Kikuo. "Japanese Women's Names in the Near Past (Part 1) | 近過去の女性名 (その1)" Bunrin. 30: 37-57. 1996.
– Japanese Women's Names in the Near Past (Part 3) | 近過去の女性名 (その3)
Unser-Schutz, Giancarla (2014). "New Japanese naming practices: Reflecting changes in ideals for children."
For late Meiji women's names, there are two good English sources: Lafcadio Hearn's 1899 essay "Japanese Female Names," and Suzuki Sakaye's 1916 rebuttal, "Japanese Female Names of To-day."
Both sources have issues. Hearn is too romantic, and makes mistakes with some of the names' meanings, but he had the advantage of being in Japan and working from Japanese sources with the aid of Japanese friends. Suzuki is Japanese and has a firmer grasp of spellings and meanings, but he was writing from memory after being out of the country for several years. He dismissed as impossible at least two names that Hearn had a printed source for, said he had never heard of a number of names that I've found in other sources, and wrote off several longer names, including names borne by students of one of the top women's preparatory schools, as fit only for geisha. My impression is that Suzuki was conservative and perhaps out of touch. However, his impressions of certain names are valuable because they're rare examples of a contemporary Japanese person's naming aesthetic.
Hearn, Lafcadio. "Japanese Female Names," in Shadowings. Boston: Little, Brown and Company, 1919. Originally published in 1900.
Suzuki, Sakaye. "Japanese Female Names of To-day," in Transactions and Proceedings of The Japan Society, v.15, 26th session, 1916-1917, pp. 1-24. London.
The Meiji-period women's magazine Jokan () printed lists of graduates (卒業生) of girls' schools by school, sometimes including details such as whether the graduate was a commoner (平民) or samurai (). Scanned copies of Jokan are available at Hathitrust. A small selection of listings: v. 11, pp. ii-iii; v. 14, pp. 82-83; v. 35, pp. 62-63; v. 38, pp. 67-68; v. 39, pp. 71-73.
Munedaka Population Register
A discussion of the 1866-1867 population record for the town of Munedaka, with lists of names and explanations of male name changes.
Edo Merchant and Craftsperson Database (江戸商人・職人データベースの検索), provided by the National Museum of Japanese History. One of many databases run by the museum. A searchable database of a 1834*** directory of merchants in the city of Edo, listing the proprietors' names, addresses, and type of business.
Plutschow, Herbert. Japan's Name Culture: The significance of names in a religious, political, and social context. Routledge/Curzon, 1995.
Confusingly written, almost aggressively alinear, and more focused on surnames than on personal names, but a useful source nonetheless.
Edo-Era Names | 江戸時代の名前
Explains some of the subtypes of Edo-era names and gives a list of terms of address.
Research Guide for Edo-Era Merchant Names | 江戸時代の商人の名前を調べる
Throndardottir, Solveig (Nostrand, Barbara). Name Construction in Mediaeval Japan. Carlsbad, New Mexico: The Outlaw Press/Potboiler Press, 1999.
Excerpts are available online, including:
An Online Japanese Miscellany: Japanese Names is a general introduction to pre-1600 Japanese names, particularly family and male names.
Rodrigues, João. Arte da Lingoa de Iapam. 1604-1608.
A Japanese grammar written by a Portuguese missionary to Japan. Volume 3 contains a discussion of Japanese names. In the linked copy, it starts on p. 412.
There are "authors" on Amazon who churn out whole lines of naming books with near-identical titles and covers. Not recommended. Highly, highly not recommended. Some examples:
A Genealogist's Guide to Japanese Names: A Reference for First Names from Japan, by Connie Ellefson
Japanese Baby Names: Names from Japan for Girls and Boys, by Jeffrey Fisher
Any standard baby name book will have a selection of Japanese names, usually limited, dated, and wrong. Baby name books have been passing around the same list of names for the past few decades, complete with weird readings and misspellings.
http://jairo.nii.ac.jp/db/sresult-jp
Zenkoku kakujou Gakkau sotsugefusei (sotsugyousei)
全國各女學校(wrong kanji) 卒業生
National Each Female School Graduates
Peeresses' School, Kazoku Jokakko (華族女学校), 1885
Joshi Gakushuuin (学習院), 1918-1947
http://books.google.com/books?id=258HIHIgXpYC&pg=PA106&lpg=PA106&dq=meiji+female+graduates&source=bl&ots=uGYc2WoPjm&sig=PrBPe_25USPmMx9i8Jmxy-vudyY&hl=en&sa=X&ei=mm99VLSXMIKUNuWxgyA&ved=0CGQQ6AEwCQ#v=onepage&q=meiji%20female%20graduates&f=false
Girls' and boys' schools: http://ja.wikipedia.org/wiki/日本の男女別学校一覧
Hashimoto, J.& Itō , N. (2011). “ Ko ” no tsukunamaeno tanjō . Tokyo: Kasetsusha
https://www.youtube.com/watch?v=n3fgHZv_5BY
Public domain data library: http://pddlib.v.wol.ne.jp/default.htm