I like staying at the Andon Ryokan - it's a beautiful (and cheap!) modern traditional-style Japanese ryokan. It's a little way out, but it's really close to a metro station (Minowa on the Hibiya line), and it's within walking distance of the Asakusa temple area. The rooms are small, but perfectly formed, and there are shared bathrooms on every floor. But it's also cheap, a unique experience, and a lovely place to come back to. The scrambled egg on toast in the morning is also really good too.