Part of the gallery and event space Hagiso, run by students from Tokyo University of the Arts (Geidai), this is a good all-rounder for meals, drinks and sweets in the heart of Yanaka. Its Japanese-style breakfast is a great deal at ¥325; later in the day there's curry, pasta, cakes and sundaes. Expect to wait on weekends as it's popular.
At the shop upstairs you can check into Hanare, a nearby guesthouse that Geidai also runs.