Shogakkan kogo daijiten
小学館古語大辞典
EA Ref: PL682 .S56 1994
51,000 words from ancient through early modern. Uses older forms of kana.

Kadokawa kogo daijiten
角川古語大辞典, 5 vols.
EA Ref:  PL682 .K32 1982
A comprehensive dictionary of 80,000 older words with illustrations. Includes obsolete terms, current words with a long history and proper nouns.

Hōyaku Nippō jisho and Hōyaku Nippō jisho / Sakuin [Index]
邦訳日辞書
Uniform title: Vocabvlario da lingoa de Iapam. Japanese.
EAC: PL681.P6 V58 1980 and  PL681.P67 V633165 1989
Based on a dictionary compiled by the Jesuits in the 16th century; useful for understanding 16th century words and pronunciation. Definitions given in contemporary Japanese.

Kindai yōgo no jiten shūsei
近代用語の辞典集成  41 vols. + 1 bekkan
EAC: PL685 .K45 1994
A reprint of dictionaries published between 1913 and 1933; each volume has its own catalog entry, giving full details about the author and the content of the individual dictionaries.  Titles for all volumes are contained in the link.

Japanese-English and English-Japanese Dictionary
J.C. Hepburn
EAC: Pl679 .H49 1872
In addition to the print version, Hepburn's Waeigo rinshūsei 和英語林集成 http://www.meijigakuin.ac.jp/mgda/kaisetsu_shubetsu.html is available online as part of the Digital Archives of Meiji Gakuin University.  An excellent resource for expressions current in Meiji Japan.