The high reviews from Trip Advisor are spot on. Hotel Century Southern Tower was by far our favorite hotel during our 2 week trip to Japan (disclaimer: this excludes our one fabulous night in the Ryokan Tanabe in Takayama, and applies only to standard hotels, not ryokans). When we arrived off our 14+ hour flight, it was so nice to find the hotel so easily, and just steps from the Shinjuku station. We took the elevator up to 20th floor, and really felt like we were in modern skyscraper Tokyo. We checked in a little early, and were able to go right to our room to take a nap. The lobby and hotel bar were both very sophisticated. Our room was on an even higher floor, and had a great view of the city. It was large, and had a nice table and chairs, and great bathroom. Everything was immaculate (well yeah yeah this is Japan). The bed was very comfy, we slept great, and therefore adjusted to the 13 hour time change rather easily. The receptionist even helped us order a pizza from Pizza-La one night. We got a reduced rate from hotels.com. Fantastic hotel.

Good location, easy access, big room compared with others hotel in Japan!
but the service of the staff just so so.

Had a stop over in Tokyo after a skiing holiday on weekend of 21/22 Jan 2012. This hotel is in a great location, easy access to the JR, Metro and Narita Express and directly opposite lots of shopping if thats your thing... This is a slick new modern hotel.
Rooms were fantastic for a Tokyo city hotel, very spacious, well equipped and super clean and tidy. Rooms start on the 20th floor and although the weather when we were there was overcast with low cloud, we had great views of the Tokyo skyline (bonus). Beds are super comfy and these rooms have to be some of the quietest hotel rooms I have ever stayed in ... anywhere. Plenty of amenties on site. Staff were great and we would definitely stay there again... Highly recommended.

For access to Ginza, I'd recommend The Peninsula.
For access to Shibuya, I'd recommend the Cerulean Tower Tokyu or the Excel Tokyu.

For Shinjuku, the Century Southern Tower is my new favorite. It's also a pretty good value choice, for a visitor that optimizes for high-rise views and easy access to everything.

+ Fantastic views, especially if you book a room facing Takashimaya and Shinjuku Gyoen
+ Relatively new construction, about 15 years old, and holding up well
+ Infinite number of shops and restaurants within easy reach. Tokyu Hands, Uniqlo, and a large number of restaurants right over in Takashimaya Times Square as well.
+ Direct transportation to all other areas of Tokyo. For my particular visit, it was a single shot event to Tokyo Motor Show in Odaiba, as well as an event in Roppongi via the Oedo line subway.

- It's not a full-service hotel, so there's no bell service for example. Perfectly fine for a lightly packed single traveler.

Pro-tip 1: If arriving on the Narita Express trains, be sure to come out the Southern Terrace exit. The hotel is closer to the platform than the connected subway station, even.

Pro-tip 2: There's a convenience store (1) on the ground level of the office tower, and (2) a 24-hour one out the back door. The in-hotel convenience store is also reasonably priced and well-stocked.

Pro-tip 3: If going to Roppongi, Azabu Juban, and Tsukiji, the Oedo line has a secondary entrance right outside the back door.

Pro-tip 4: For accessing the JR Yamanote Line, heading towards Harajuku and Shibuya, walking over to the Yoyogi station is probably faster than going into Shinjuku station.