Cozy Places to Stay for Foreigners in Japan

The very strict laws about hotel licenses in Japan require all serviced apartments to rent from only one month or longer. These are fully furnished, have cleaning service and best of all a 24 hour toll-free hotline in English so that if you need assistance during your stay, there is always someone to help. I worked at Space Design Inc., that runs the BUREAU and B-SITE serviced apartments in Tokyo and Yokohama (total of 1000 plus apartments) and their service is perfect for single business people here on short to extended stay. Their rates start from just under 200,000 yen per month with everything included, so it would be good for students on summer programs, etc., as they are in very safe areas of Tokyo. When you look for a serviced apartment, be careful of hidden costs like move out costs, separate utility fees, etc. Space Design and Relo Japan (Japan residence in Nagoya and Yokohama) are good ones I know of based on personal experience.
http://www.space-d.co.jp/en/