My husband and I have been to Tokyo numerous times, and we always come back to the Tokoyo chain. Their Shinjuku Kabuki branch is our favourite. Here are the pros and cons:

Pros:
1) Friendly staff - Fluent in English, and some in fluent Mandarin
2) Clean and tidy - as with all Japanese hotels/home stay
3) Free breakfast - Japanese style, including rice balls, miso soup and pickles
4) Free internet at the lobby
5) Discount on weekends - 20% off Sunday + holidays for Tokoyo Inn Cardholder (foreigners accepted, you can sign up on the spot, annual fee = ~$16 USD, depending on the duration of your stay, the savings may be worth it)
6) Adjacent to Kabuki - night life, for ladies and guys! And super good ramen stalls that stay open late
7) Safe neighborhood - people in suits/evening gowns on the street are looking for business only, not trouble. No one bothers you if you don't show any interests.
8) Shopping - lots of shops about 2 blocks south of hotel, including brand new department stores like Isetan, Mitsukoshi. Guys may find interesting gadgets in Big Camera and Yodobashi Camera stores (Like Fry's in the US, but about 5 - 8x larger and more varieties). Basement level of all upscale department stores are filled with food stalls. Look for great bargains on daily fresh items (eg. tempura, sashimi, karaage, salads, sandwiches, etc.) ~2 hrs before store close. Prices keep dropping every 15/30 mins until gone or store close. Great price for quality cooked food! (Not sure if you want the sashimi, they still looked fresh, but we worried how long it's been out)

Cons:
1) 15 mins walking from JR station - a bit of walk if you're carrying luaggage, but not totally unmanageable
2) Difficult to locate first time - a bit challenging for first time visitor. Street names in Japan are very hard to find, but at least the locals are very willing to help
3) Rooms are small - our double room is barely enough to hold 2 single beds and 2 pieces of check-in luggage. Tiny bathrooms too
4) Dehumidifier in bathroom really dries you up!! My husband made the mistake of leaving it on before going to bed. We both dried up like prunes overnight, waking up in the morning with super chapped lips and skin
5) All TV channels are Japanese only

Overall, the pros totally outweighs the con. Like I said in the beginning, we always come back to Tokoyo Inn whenever we're in Japan.

Toyoko Inn was great. Cheap, clean, nice breakfast included. Wifi only available downstairs but the rooms have a cord to connect laptops to internet. Good location, short walk to the train station and lots of bars and restaurants around. The rooms were quite small but not bad for the price. Book early to avoid disapointment!

I was pleasantly surprised at how much I liked this hotel. My room was small, but everything was clean and cozy. The bathroom was very nice with amenities and an electric toilet seat that is so popular in Japan and Korea. It is centrally located in Shinjuku near plenty of shopping, restaurants, and the subway. A Japanese breakfast is also provided for guests. I would stay at this hotel again if I ever return to Tokyo on business.

Toyoko inn Kabukicho is a great place
close to everything
close to shopping
close to all kinds of Japanese restaurats
Close to subway
very friendly staff
very helpful staff
Free WiFi
Free Internet
Free breakfast
Clean and decent budget hotel