Contrary to popular belief that Tokyo is a VERY expensive city to travel in or live in, there are actually many budget options for cheapo travellers like me. In Tokyo, I have stayed in the very best hotels as well as the budget accommodations. Of course, there are the hotels that'd cost over SGD400/night but there are also many that are in the range of less than SGD200/night.
And unlike poor quality budget accommodations that you often find in some asian countries, even the "star-less" inns/motels in Tokyo are extremely well-kept, clean and thoughtfully & tastefully furnished.
While there are some cheap hostels or budget ryokans that'd cost less than JPY4000 (~SGD68), or even cheaper capsule hotels, I'd usually stick to the mid-range western style budget inns/motels with ensuite and my budget is normally around JPY7,000-8,000/night (SGD119-136).
Here are some photos of the budget motel rooms that I had stayed in...although tiny (most of the normal rooms in 3-4* hotels are not very much bigger though), they are usually very cosy and comfortable.
A few things to note, first, double beds are tiny (just slightly broader than a single bed) and really not meant for 2 persons unless you don't mind suffering many sleepless nights! Second, if you are uncomfortable stripping in front of others and bathing at the public bath, you might want to avoid accommodations without ensuite. The bath area is often without cubicles/doors. It is probably just a row of showerheads and taps fixed on the wall and you have nothing but a tiny stool to sit your naked butt on to bathe!
This is a single-bed room in Toyocho Vista Hotel which is just less than 50m walk to the Toyocho Stn. Think I only paid around JPY7,000/night Yes, it's tiny. This is the other end of the bed.
This is another motel with double bed. Think I only paid around JPY6,000/night.
Most of the ensuite are small but as you can see, still very well equipped.
Below is a list of some budget accommodations as well as budget hotel portals if you are travelling on a shoestring:
Tokyo Inn http://www.tokyo-inn.co.jp/en/index.html
TOYOKO Inn http://www.toyoko-inn.com/eng/
Japan Hotel Net http://www.japanhotel.net/
The Budget Hotels In Japan http://www.e-otomari.jp/~english/
Sakura Hotel http://www.sakura-hotel.co.jp/
Nishi-Shinjuku Hotel http://www.nshotel.com/
Super Hotel http://www.superhotel.co.jp/
Rakuten Travel Hotel Bookings
Tokyo Capsule Hotel Listing http://gojapan.about.com/cs/accommod...yocapsule1.htm
Japanese Guest Houses
Kimi Ryokan (Ikebukuro - Tokyo) http://www.kimi-ryokan.jp/index.html
Andon Ryokan (Tokyo) http://www.andon.co.jp/