Like The Don, I commute pretty much daily here in Tokyo and have to agree with him. However, over the past few months I have been hearing mumblings of people saying they are starting to crack down on bicycles running reds/stop signs etc. But, I have yet to know or see anyone who has been charged with anything other than having their mamachari trucked away from the train station.
The only thing I would highly advise against, especially as a foreigner is dont have a beer and cycle. It is apparently looked upon and ranks up there with driving under the influence. But again, never heard of anyone being charged with this.