Today I was surprised that a friend of mine, who has been translating manga for several years now, didn't know of any online dictionaries other than Jisho.org and Google translate! If this is the case, then there must be many people who don't know how many great sites there are online to use as a resource when reading, translating, or studying Japanese! The following is a list of sites I personally have used to help me read and translate Japanese. If you have any good resources that are not on this list, please leave a link in the comments!
Jisho.org - I think that almost everyone knows this site. It is the most comprehensive and English-friendly online dictionary. You can enter japanese words in romaji, hiragana or kanji. Probably the best feature of this site is the kanji look-up tool, "kanji by radicals." If you haven't specifically studied radicals (I never did) it might be hard at first but if you look at the chart you can usually find at least one or two elements that appear in the kanji you are trying to look up. At the bottom it displays a list of all the possible kanji featuring those radicals, and the more you can add the more it narrows down the list of possible kanji. The more you use this feature, the faster you get, and I'm told it can be really quick and easy to look up kanji this way once you are familiar with identifying radicals in a kanji and finding them on this chart.
Goo Dictionary - My 2nd year Japanese teacher and the head of the undergraduate Japanese department at my university both swear by this site. It's a Japanese site so it's not as user-friendly for the beginner, but it's not all that hard to use. To search from Japanese to English, click on 和英辞書 and to search from English to Japanese, click on 英和辞書. Goo Dictionary is better than Jisho.org when it comes to phrases, both in English and Japanese. Jisho.org has the most common ones, but Goo dictionary has a greater number of them. Another useful feature is the Japanese Thesaurus, 類語辞書.
Zokugo Dictionary - This is a Japanese-Japanese dictionary for colloquialisms. You'll need to have a good grasp of Japanese to use it effectively, but you can often find phrases here that don't appear in Japanese//English dictionaries.
Weblio - To be honest, I'm not really sure why but I think weblio is my favorite online dictionary. I don't use jisho.org much anymore, and I am more partial to weblio than to goo dictionary. First of all, instead of having separate Japanese to English and English to Japanese dictionaries, they're both together under the 英和和英辞典 tab. This site also has a Japanese Thesaurus (類語辞典) and even a sign language dictionary (手話辞典). I think what I like about this site is that when you search a word, it brings up SO much information related to that word: multiple definitions, common phrases, translated sample sentences, synonyms and related words.
Jaded Network - This is the best SFX dictionary I've found. Technically, anyone can contribute to it, so it continues to add new information daily. To be honest, I rarely look up SFX any more because the usage of sound effects is so dynamic that I don't think it's really possible to directly translate them most of the time. However this site can be a good reference if you are new to the world of Japanese SFX, or if you just can't think of a good way to phrase that sound in English.
Onomatopoedia - A Japanese-Japanese SFX dictionary component of goo dictionary.
Kotobank - I don't actually use this very much, but it's on my bookmarks list. It's a Japanese-Japanese dictionary.
IMABI - I only stumbled upon this site in the last year or so. It's a thorough explanation of pretty much all the grammatical structures and conjugation patterns of Japanese. I think it's a bit more comprehensive and higher level than Tae Kim's Guide to Learning Japanese. Also includes some lessons in Classical Japanese.
Tae Kim's Guide to Learning Japanese - I used this site a lot when I first started translating manga, to look up grammar patterns I came across that I hadn't learned in class yet. The explanations in English are easier to understand than those at IMABI, but I think that IMABI has more material.
SLJFAQ Kanji Look-up - Basically the same thing as Jisho.org's kanji look-up tool. It may come in useful if Jisho.org's server crashes, or something.
Tangorin - Another English-friendly Japanese-English dictionary. Sometimes I've found words here that didn't show up on Jisho.org. It seems that this dictionary combines the entire libraries of several other popular dictionaries into one search engine. The Japanese Names dictionary is also a bit better than jisho.org's.
Yomikata wa - This is a very simple tool that saved my @$$ last semester. It does only one thing -- give the hiragana and romaji reading of any kanji you plug in. It does a phenomenal job with people and place names, which most other dictionaries don't include. You can only input kanji, so if you're not copy-and-pasting from online newspaper articles like I was, you'll have to look up the kanji individually so you can input them into the search. This site is not ALWAYS accurate, because people and place names often have irregular readings, but this dictionary lets you know when it's not too sure about the reading!
Rikaichan - An addon for Firefox. If you hover over a kanji with your mouse, a pop up appears that shows the reading in hiragana and the English definition. This makes reading Japanese websites SO much easier. You still need to know grammar, but it essentially reads the kanji and translates all the vocab for you. According to the website, you can set Rikaichan to translate the words to German, Russian or French as well, instead of English.
Rikaikun - Rikaichan adapted for Google Chrome. I use this add on every day! I think it makes me a bit lazy, though. Also, when I'm not trying to use it, the pop ups get really annoying so I have to turn it off. It's no good for slang or people/place names, so don't both trying to use it on facebook (lol).
Hiragana Megane - In case you are using a browser other than Firefox or Chrome, or you can't/don't want to install an add-on, or you don't want to see the definitions of kanji, just the readings, you can use Hiragana Megane. You copy and paste the URL of the Japanese website into Hiragana Megane and it displays the site in browser with tiny hiragana over the kanji. You'll have to know or look up the meaning of the words, but it's a lot easier now that you know the readings!
The Ultimate Guide to Reading Food Labels in Japan - This is just a bonus. A useful blog post with an in-depth explanation of the nutrition facts labels on Japanese food products.