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I will endorse jisho.org as I have used it extensively. I have also found the Firefox Add-on Rikai-Chan and the program JLookUp to be quite helpful. Both were recommended to me by my upperclassmen. Both are free.

Rikai-Chan is a dictionary you can use by right clicking, turning it on, and then highlighting the Japanese you don't know.

And JLookUp is a dictionary program that sits on your desktop so it can be used when offline. It has a Japanese-English, English-Japanese, and Romaji-Kana functions. It does have dialect and archaic words so you have to be on the look out for them. It also has a Kanji Look Up function that allows you to build the kanji you're looking for out of radicals. It helps quite a bit when translating a kanji with an unknown reading on the fly. if anything, get it for that function alone.

Rikai-Chan

JLookUp Download page

I used to use the Jim Breen Jdic in high school:

http://www.csse.monash.edu.au/~jwb/cgi-bin/wwwjdic.cgi?1C

It served its purpose.

Also, if you have an iPod/iPhone/iPad, I've found a few free apps that work nicely:

WordPowerLt
JLPTStdyFree
JpCard
Kotoba! (Based on Jim Breen)