There's a chain of bakeries called "Good Morning" and one branch is in my neighborhood. They also sell their baked goods on consignment at supermarkets (such as Ito Yokado) so you can get their offerings even if a cafe or bakery is not in your immediate area. While there are tons of excellent bakeries in Tokyo, this place has a koshian (red bean paste) bread which is sublime. It's soft, lightly sweet and incredibly delicious. It looks like marble cake, but it has texture and subtle flavor delights that might convert even the most red-bean-hating person to the appeal of this traditional substance. Good Morning also has a fantastic maple pastry for the most conservative of foreign eaters and is one of the very few bakeries to sell authentic and well-made sourdough bread.
The aforementioned koshian bread. So good, even if you aren't a red bean fan.
I'll miss Good Morning Bakery, and the delights it offers me on a regular basis.