Good location and a good price.
I stayed for 6 nights at the Hotel Listel Shinjuku and then left my luggage there while on an overnight trip to Osaka. I returned and stayed these last 2 nights. The 2nd room was a little roomier than the first room, but both rooms were clean, staff was courteous, friendly, and efficient. This is a Japanese style business/tourist hotel for the budget minded traveler and I would highly recommend it based on price, location, and staff. If you have a lot of luggage you will want to take a cab from Shinjuku station to the hotel, it's only 700 - 800 yen, but its still close to central Shinjuku and not far from the Marunouchi Subway line.
It helps if you speak Japanese, but that is really not necessary either. Free high speed internet connection in each room. I highly recommend this hotel if you don't want to spend a lot of $$ in Tokyo for a room. Just remember the rooms are small by western standards.