Handwritten Kanji Search http://kanji.sljfaq.org/
This little device has saved my bacon a few times. You use your mouse to literally draw the kanji you are looking for. It's is dependent on stroke order, but is also quite forgiving if you get a couple of strokes out of order.
Multiradical Kanji Lookup http://kanji.sljfaq.org/mr.html
This is from the same site as the handwritten lookup, only you select parts of the kanji (radicals) and it narrows the list down accordingly. There are a few of these around, however I like this one as it throws a few 'unofficial' radicals to the mix.
Lite Text Gloss http://www.csse.monash.edu.au/~jwb/cgi-bin/wwwjdic.cgi?9T
With this site you simply type or paste in words you want looked up, and it spits them back out with Japanese readings and English meanings. It comes in handy now and then.
Space Alc http://www.alc.co.jp/
Space Alc is an online dictionary with user submitted (I think) definitions and example sentences. I mostly use it like a thesaurus; looking over the various ways a word can be translated in different contexts. Be warned though, some of the examples and definitions it gives can be very context specific and will not work outside of that given context.
Google Image Search (you need the url for that one do you?)
This is an old trick of the trade. Usually used as a last resort, when you just can't figure out what a word means, pop it into google image search (or any image search for that matter) and the images it brings up will normally give you some clues to the words meaning.
This is dictionary program which uses the EDICT family of dictionaries. It's nothing special, really, except for that fact that it works offline. It's just a program that sits on your hard drive. It's not an amazing piece of software by any means, and seems to crash a lot, but if my internet goes down it's always there to help me out.
I would be interested to see what kinds of sites/tools that people are using, so if you have something useful, post it.
(First person to mention google translate gets a complimentary kick in the teeth)