In general, I agree that Japanese bread is pretty bad.
But it seems like recently (the last few years) there has been a huge boom of artisan bakeries, especially in Kyoto.
I very much like the bread at eze bleu, on the south side of Imadegawa between Teramachi street and Gosho. It’s on my way to work, and they have several really amazing breads. My favorites are the rye with dried cranberries and pine nuts, and the graham flour bread. They also have an unusual and delicious bagel with orange peel in it.
http://www.onozomi.com/univ_gourmet/topic05_d_eze.html
Another bakery I love for their Bagels. Bagels in Japan are such a rarity at all, but this shop does them quite well, although they do seem to like some rather strange flavors. I keep trying to convince them to start offering a pumpernickel, but for now I settle for poppyseed or grains.
It’s called Browny, and is on the north side of Kitaoji street, between Vivre (at Karasuma) and the Kamo river. Their mentaiko france is really great too!
http://www.browny-kyoto.com/bagel/bagel.html
One more hidden gem is this little german bakery up near Kamigamo Shrine. It’s really hard to find, but totally worth looking for!
The name appears to be Hunaudieres or Yunaudieres depending on where you look. This is the only place I have found REAL pumpernickel in Japan. They have great german bread and french pastries, as well as apparently once a year or so making traditional pretzels. The owner said that he doesn’t do it more often because the lye is too hard on his hands!
They also sell homemade yeast and some other baking ingredients.
http://www.leafkyoto.net/shops/view/5159