My favorite place to stay in Tokyo is The Juyoh Hotel, http://www.juyoh.co.jp/index.html The Juyoh Hotel is a wonderful, clean, safe, comfortable and friendly hotel for travelers on a budget. It is a place where you will experience the Japanese way of living, as well as meet interesting and friendly travelers from all over the world. The lovely proprietors and hosts are Toshi-san and his wife, Sakura-san, and everyone who stays at The Juyoh Hotel is treated as a member of the Juyoh family. The young staff are multilingual and always friendly and helpful. I love to stay here because the milieu is so stimulating and a lot of fun.
It is one of the most reasonable places to stay in Tokyo for the short term, and also offers the option of reduced Guest House rates if you plan to be in Tokyo for an extended period.
For further information, you can read about my Juyoh Hotel experience in my book, The Adventures of the Wanderer. Be sure to mention me to Toshi-san and/or Sakura-san when you stay there, and you will be well taken care of.
*Note: I write about people, places and things that deserve to be written about for one reason or another, and I am not being paid to do so.