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Dictionaries 辞典 字典（じてん）
These tools help turn your mouse into a dictionary. It is very addictive and can really help speed up your reading - but the lack of pain may mean that you don't remember kanji or words as well as when you look them up one by one.
Collections of Dictionaries
I think that these are my top picks for free online dictionaries. You may have other suggestions, please let me know and I'll add them.
Very nice collection of more than 50 dictionaries, each one provides source information.
Collection of dictionaries: kokugo, ruigo, waei/eiwa, shugo (sign).
Yahoo! Japan Dictionaries
This set of dictionaries (J, thesaurus, JE, EJ,) can be searched individually or all at once. It also offers two dictionaries for J and JE/EJ so you can see variations.
On'yaku no heya 音訳の部屋
This is a very interesting collection of resources for people who read aloud to the blind. It includes a lot of readings that people would just guess at if they were reading silently, therefore a good tool for Japanese language learners.
Collection of many dictionaries and two encyclopedia (Japanese and Kodansha's Encyclopedia of Japan).
Sometimes you really need to use a special dictionary to find particular words. Here are some examples: onomatepeia, slang, etc.
Giongo, gitaigo jiten 擬音語・擬態語辞典
Call Number: UM East Asian Reference / PL685 .A73
A Thesaurus of Japanese mimesis and onomatopoeia
Call Number: UM East Asian Reference / PL685 .C43 1990
Ruigo Daijiten 類語大辞典
Call Number: UM East Asian Reference / PL667 .R85 2002
Ingo Daijiten 隠語大辞典
Call Number: UM East Asian Reference / PL697 .I54 2000