Hotel Villa Fontaine (Shiodome, Roppongi and other locations) http://www.hvf.jp/eng/
Popular hotel with reasonable charge which includes breakfast. Convenient locations, large room, free LAN internet.
The Japan-United States Educational Commission (JUSEC)
207 Sanno Grand Building, 14-2, Nagata-cho 2-chome, Chiyoda-ku, Tokyo, Japan 100-0014
Phone 03-3580-3231