Shinjuku New City

Stayed there just 3 nights. The staff were very helpful.

The room was not very big, but certainly comfortable enough for myself and a freind (twin room)
We had to pay at check-in (rather than at check-out), however this is normal at "business hotels" in Japan.

It is about 15 minutes walking to Shinjuku station. The biggest station in Tokyo where there are quite a few Metro/Subway trains. Making it easy for getting around.
They also provide a Shuttle from the station to the hotel.

There's also internet access in the lobby at 100 Yen (0.80US) for ten minutes.
In addition, there's free broadbad in the rooms. Not wireless though, however they will provide you with a network cable if you don' have one.

Overall, a very good location if you're just visiting the city. You're much better off in this area than say "Roppongi" where you will be harassed every five minute by touts trying to get you in a club.

Unique Quality: Internet access in the lobby.
Free broadband in the rooms (wired NOT wireless)

Directions: Business/Tech/Shopping District

My stay at the New City Hotel was pleasant. The beds are comfortable, not hard and stiff, so you can get a good nights rest. There are televisions in every room. The bathrooms are a bit small, but they're manageable.
The restaurant in the hotel is called "Mermaid" Restaurant. I ate the buffet. There was a decent amount of selection, and all of the food I tried was good!

Unique Quality: It's located near Shinjuku's Park and the government building.

Directions: In Shinjuku, near the park and across from the government building.