(Note: I'm going to assume you know basic Japanese phonetics and the base writing systems with each of these. If you need a primer, you know where to look)
Denshi Jisho and Nihongo Master
Both of these sites are excellent places to see how the different vocab you pick up is used in a sentence(assuming it has one, of course)
Nihongo Resources(and its redesigned iteration)
One of the very best places to pick up more about different grammar points, and is where I got my start in the language, in terms of online resources
NHK Web News Easy
For when you want to practice your listening skills and how well you can interpret the intent of a statement
A good place for beginners of the language to learn about Japan's culture and learn some basic Japanese words and phrases
Crunchyroll, Hulu, KeyHole TV, and elsewhere
If you wanna hear the language in a more colorful context, you can always watch the media of the country and take it in as it is, so you can better grasp how the sounds work and be entertained at the same time!(KeyHole TV even gives you a direct live feed from the country! Warning: choppy feeds ahoy)
The Japan Times
An English Language online publication which a wide range of info concerning Japan and Japanese culture(along with a few other things from other countries for those in Japan wanting a taste of home)
A blog(and about as biased as you'd expect a blog to be, my own, included) offering more intimate insights into the country's culture and interaction with other countries, as well as subtitled videos of news programs in and around Japan
A blog offering a more detailed insight into some of the politics, politicos and lesser known cultural aspects of the country-for example, it was through that blog I learned that one of the members of the Diet of Japan, 蓮舫(れんほう), was, in her younger days, a gravure[Japanese variant of a pin up] model.(If you don't believe me, you can check this Not Safe For Work video of her) More upfront & inclined to conservative points, so those with more delicate/strongly liberal sensibilities take caution.
Offers a great insight into the culture developed in the city of Tokyo, as well as elsewhere(and also covers other major Asian cities, should be so inclined to give those a peek)
A blog focused on giving a intellectual insight to things few ever speak of about Japan, like the stranglehold Johnny's(management company) has over Japanese boy bands and the graphic arts of the culture.
Jlist Side Blog and Danny Choo
Walks the line between 'Those Crazy Japanese!' and treating the culture with respect very well, and continues to offer their own distinct knowledge about the society, such as Japan's concept of a childhood friend and How Japan Shaped the Course of Danny Choo's Life)
Turning Japanese(no, not the song!)
A great resource if you're looking to spend your life in Japan and are wondering what's involved in doing so (word of warning, though, this means you'll need to give up your current citizenship for a Japanese one and your current name for a Japanese one, and if you have any kids there, they'll have to choose one or the other when they hit 22)
The food tales of a well traveled Girl of Japan, along with very tasty recipes and her unique insights into the culture(including how rice is cooked in Japan)
Festivals in Japan
A listing of all the festivals taking place across Japan at any given month. Very good to finding out where to get your party on when you go over there!