Levain near Yoyogi and perhaps the Jensen Danish bakery nearby for Graham Bread and their cookies (only available in the cooler months). Have to disagree with mjm about Viron as their viennoiserie is a whole lot better than the other "French" chains. D'un Rarete has a great buttery brioche loaf, as does their sister shop 365 Jours in Yoyogi Hachiman. Great for making french toast (without the lines).
I had a morning set served at 5PM on an aircraft recently.......bizarre !