Colors Café in Osaka has an impressive all you can eat bread buffet. Served in cute baskets, the ones you should definitely try are the matcha, whole grain, tea bread and the bread with apples (something like apple pie but closer to a bread version). At night, Colors also serves dinner.
Rojiusagi is a small residence near Hanamikoji Dori in the Geisha district of Kyoto. They serve traditional Kyoto breakfast, Japanese home cooked meals and even western breakfast. The owner manages and cooks the food by herself, it has a garden and a small library of books, the seats are on the floor covered with Tatami mats but a seat by the bar is available too.