Being new and unfamiliar in Japan, not to mention having a huge language barrier, we stayed in hotels right next to the train stations.
In Tokyo, we stayed in Century Southern Tower Hotel, right next to Shinjuku Station, the biggest and busiest train station hub in Japan. The hotel was overbooked, instead of single room, we had to take the deluxe double room, the room rate was a whopping 29600 yen, or US$300-ish a night. We learned later that we came to Tokyo at a bad time, it was the week of the universities' entrance exam, most of the high school grads around Japan flock into Tokyo.
This Southern Tower is kind of interesting though. The entire building is 35 floors tall. The first 4 floors are shops, 5th to 18th floor are office floors, 19th and 20th the hotel lobby and restaurants, and 21st onwards are hotel rooms.
Overlooking the Shinjuku Station, lobby view
Overlooking Times Square/Takashimaya, room view
For some reason I forgot to take photos of the hotel room...
We stayed in the Richmondo Hotel in Fukushima, right next to the Shinkansen station (bullet train). Being out of Tokyo, we were able to get single rooms, and the rate here is much cheaper, 9600 yen a night, or US$100-ish. I suspect that hotel in Tokyo, even with single room, the rate won't be this.
I do have some photos of the room here.
This is what a single room in Japan looks like.
The toilet bowl comes with an interesting gadget. It keeps the seat warm, and has 2 water spraying mode to help you clean your ass after doing big business. I wonder why the American hotels do not come with this convenience.
Conclusion: Accommodation in Tokyo is freaking expensive!