1. BIO http://www17.ocn.ne.jp/~bio/
My favorite are these three... pain de campagne, basil&cheese, and fruits&nuts. And I love Mr. & Mrs. Ishimoto, the owner of this bakery!
2. La Boulangerie http://www.laboulangerie.jp/
My favorite are sweet Danish pastries and "fougasse"!!!! This fougasse is soooo delicious! These are not wild yeast breads, though..... Chiaki-chan, the owner, is a very cheerful and sweet girl. I sometimes go there just for chatting with her! Sorry to bother you, Chiaki-chan!
3. Kinuta http://www.kinuta.com/
All of these are wild yeast breads. Very tasty.
