The best soba is made at Tamawarai 玉笑. Note that there is usually a long wait. (It's that good!).
My favorite ones:
- Kanda Matsuya (near Akihabara)
- Muromachi Sunaba (Kanda)
- Ueno Yabusoba (Ueno)
- Namiki Yabusoba (Asakusa)
If you can drink, enjoy small dishes such as Dashimaki Tamago (Japanese style omelet) and Itawasa (fishcake and wasabi) or tempura with drinks (sake is the best!) before soba.