If you are soba freak, go to Shirogane, hidden holy land. One of best is Muho near Shorogane Takanawa st.
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The best kushiyaki @ Shinagawa st. is Marumiya in Shuwa bldg. 2 min from Takanawa exit by only ¥3,000
We are missing St. Martin and Anguilla. Samanna and CapJulca always give us great power.
If you like more secret place, try Rogetsuan or Nioka, next best but ones of top in Japan.
If you are in the mood of Chinese, go Osho of Gyoza (Dumplin). 1,000 yen will satisfy you including beer on tap.