You can find izakaya (Japanese style bar) in almost any part of Tokyo. Near most major stations, you'll find whole streets of hole-in-the-wall places. One celebrated example is Shinjuku's Golden Gai.

I guess it's unlikely that many flyertalkers will find themselves in Kachidoki... but if you ever stray there, I would recommend stopping by Bar Tin. It's one of the tiniest and friendliest bars in town. Standing room only for about eight customers.

For more Japanese flavor you could try any of the excellent sake pubs that are recommended in this article by John Gauntner:
http://www.bento.com/drinks/sake01.html

And... many more bar reviews in Metropolis:
http://metropolis.co.jp/tokyo/530/bars.asp