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.
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RikaiYou have 2 choices, either input a URL and Rikai will follow you wherever you go on the web or copy and paste in text to see readings and definitions.
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Jim Breen's WWWJDICThis is a favorite of many because of the extensive word lists. You can also look up kanji by a variety of indexes.
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.
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KotobankVery nice collection of more than 50 dictionaries, each one provides source information.
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WeblioCollection of dictionaries: kokugo, ruigo, waei/eiwa, shugo (sign).
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Yahoo! Japan DictionariesThis 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.
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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.
Subscription Databases
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Japan KnowledgeCollection of many dictionaries and two encyclopedia (Japanese and Kodansha's Encyclopedia of Japan).
Specialized Dictionaries
Sometimes you really need to use a special dictionary to find particular words. Here are some examples: onomatepeia, slang, etc.
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Giongo, gitaigo jiten 擬音語・擬態語辞典Call Number: UM East Asian Reference / PL685 .A73
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A Thesaurus of Japanese mimesis and onomatopoeiaCall Number: UM East Asian Reference / PL685 .C43 1990
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Ruigo Daijiten 類語大辞典Call Number: UM East Asian Reference / PL667 .R85 2002ISBN: 4061232908
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Ingo Daijiten 隠語大辞典Call Number: UM East Asian Reference / PL697 .I54 2000ISBN: 4774402850