I'm sure you're all familiar with this one. YouTube has been gaining popularity in Japan, so there are a growing number of videos that you can make use of. As you probably know, commercials are one medium easily found.
You can also search for songs or music videos by Japanese artists.
Because YouTube is subject to copyright law, you may have difficulty finding entire shows or movies, but there are still interesting cartoons and skits for your viewing pleasure.
This website hosts a ton of anime and J-dramas. I admittedly haven't explored its murky depths very extensively, only poking my head in now and then to check out a little J-drama action. There is a limit to the number of videos you can watch per day as an unregistered guest, but you can sign up for free to watch an unlimited amount of videos. Unfortunately there aren't very many with Japanese subtitles, but I suppose you get what you pay for.
3. Niko Niko Douga
The most promising of the three, and the most intimidating to use unless you're comfortable navigating Japanese websites and doing searches in Japanese. Niko Video is a Japanese website, so no English available. Again, there's a lot to look at and I haven't fully explored all that's available. These days I mostly use this website to watch Japanese dubs of the Simpsons. The Japanese voices are surprisingly quite good. To use this one you must register a free account.
* Tofugu recently put up an article about using subtitles to study Japanese. He makes some good points about active vs. passive studying. Using the resources above is a good idea in any case, but of course you'll get more out of them if you're using them for active study. That said, enjoy learning!