Eijiro is a more comprehensive Japanese-English dictionary than JWPCE. It is a cheap dictionary with a huge amount of entries. In many ways it is the perfect dictionary to complement edict. The dictionary data in Eijiro comes from EDP. Eijiro is actually a suite of dictionaries--the two main ones are Eijiro, which has 1.66 million English-to-Japanese entries, and Waeijiro, which has 1.94 million Japanese-to-English entries (as of ver. 116, June 17, 2008). Eijiro also includes separate dictionaries of example sentences, abbreviations, and acronyms. It was made and continues to be updated by a society for professional translators; as such, it's especially rich in difficult and obscure terms, colloquial expressions, and technical terms. It is free to use online at http://www.alc.co.jp/. You will find here many amusing entries and colloquialisms not found in commercial dictionaries. Eijiro is made for translators, so it assumes you already know basic vocabulary. Sometimes if you search for a fairly basic word, you won't find it--in that case, look in Edict. To use the Eijiro on a desktop/Laptop you need to have a PDA reader software such as Personal Dictionary (PDIC). PDIC is the default dictionary reader for Eijiro.
The middle-size versions of the Kenkyusha dictionaries are free to use here: http://kod.kenkyusha.co.jp/demo/form.jsp
It is a Japanese-Japanese dictionary. The Koujien dictionary is for Japanese people to lookup Japanese words. As such there is little to no English in it. So, for most students they probably don't need the Koujien dictionary in their initial years. But, at some point in your later studies you should probably start using a Japanese dictionary. You can also buy it in book form.
This is actually an all free reading program. It is available for Windows only. It has been in short development with no update since the end of 2006, but is still workable enough. What this program will let you do is copy a passage of Japanese text into it and have furigana as well as the English meaning of words written in between the lines. You will be able to make sense of long passages extremely quickly this way and find the sections which are relevant. At the bottom of the text processing area (not the toolbar above) there is a button marked “Dictionary”. Click on this and the currently positioned word will have its dictionary search displayed in full. You can also search here in Japanese and English, it will even accept conjugated typed words. The best part of the dictionary is that some of the words will have example sentences (check the “Examples” button below the dictionary area). This is incredibly useful for understanding new word usage. Wakan uses the free “edict” dictionary by Jim Breen of Monash University for its translations.
JISHOP is yet another Windows based dictionary software designed by Vadim Smolensky. It presently includes around 4300 entries and has a plan to increase it to 6355 single kanji from the computer set JIS X 0208-1990. It boasts about its original look-up system which indeed is quite attractive and useful. Its unique features include kanji drill, search by traditional keys, magnifying kanji, codes, indexes and keys. JISHOP also contains a phonetic dictionary. It stores jukugo (compound words) used in kanji dictionary entries, to illustrate the usage of characters. The phonetic dictionary can be also used independently to find compounds by their kanji writing, reading or meaning. JISHOP database amalgamate the best of Japanese-English lexicography. Numerous paper sources and resources from the Internet were used to fill it up. The main emphasis of dictionary entries is on the actual practical usage of kanji in modern Japanese. If you are serious about learning kanji, this program is invaluable.
As for me, Kenkyusha's New Japanese-English Dictionary (新和英大辞典version) is the best. Which one is your favorite?