Weblio 英和・和英辞典 including Kenkyusha dictionaries.
Kotobank : search from 99 dictionaries and encyclopedia at once.
辞典横断検索 Metapedia : the site allows to search 551 reference books at once.
語源由来辞典 Japanese Etymological dictionary
古事類苑 Koji Ruien (1933) digitized by Internet Archive.
古事類苑全文データベース Koji Ruien full-text database About 10 % of 67,000 pages are digitized in this on-going project.
Digital Dictionary of Buddhism 電子佛教辭典 ID
Edited by Charles Muller, the dictionary provides English definitions for Buddhist terms in a range of languages, including Chinese, Japanese, Korean, Pali, Sanskrit, and Tibetan, as well as pronunciations. It includes A Dictionary of Chinese Buddhist Terms : with Sanskrit and English equivalents and a Sanskrit-Pali index, compiled by William Edward Soothill and Lewis Hodous.
JAANUS: Online dictionary of Japanese Architecture and Art Historical Teminology Compiled by Dr. Mary Neighbour Parent
Some 20 reference books below are seachable at once, or individually.
日本大百科全書（ニッポニカ) this encyclopedia search provides relevant web links as well.