Breakfast
Vie de France is a bakery chain found almost everywhere on the main island of Honshu. Mostly located in train stations, it's a solid option for a set breakfast. Depending on the location, sets cost between ¥470 and ¥650 and include a savoury item (egg omelette, hot dog, warm tuna toast, egg sandwich, ham and cheese sandwich, etc), a drink, and sometimes a small extra, like a banana or a yoghurt. The coffee is brewed siphon-style and has a good depth of flavour.
Pastries
Their full range of sweet and savoury pastries is well-priced, so feel free to build your own breakfast instead of taking the set. Expect classic French shapes like croissants and pain au chocolat alongside more Japanese-leaning options such as curry pan and melon pan. My favourite: the caramel cheese bar (カラメルチーズバー), a sweet milky cream cheese Danish.