http://www.viki.com/ has some in a variety of languages, but many in Japanese. The subtitles are likewise available in several languages, sometimes including the transcripted original Japanese. I'm not sure how good the content is though, since I only saw ドラマ which isn't my thing.
They seem to be a legitimate business with VC funding, so I don't think it's a piracy site, which is a plus.
http://www.youtube.com/user/tokyomx is a news channel available on YouTube. The really nice thing is that many of their videos have Closed Captioning in Japanese (click the CC button on the video). So you can read the Japanese as they speak it.