Originally Posted by jonbai

Not sure this would necessarily suit your style of travelling, but when I was in Tokyo, I had fun staying in internet cafes, capsule hotels and urban camping!

It's actually quite common for people to stay overnight in internet cafes, they even have sofa beds and showers which you can use (as well as free drink refills). It was the cheapest accommodation I could find available (apart from camping or couchsurfing) and quite popular with the cyber-homeless (http://en.wikipedia.org/wiki/Net_cafe_refugee).
While in Tokyo, I would take a small bag containing several changes of clothes and shove my main backpack (a MEI voyageur) in the largest coin locker available at one of the metro stations, leave it there for several days. I could then roam around the town and just find an internet cafe wherever I ended up at the end of the night!

As for the capsule hotel, I avoided the touristy ones and found one in a downtown working class area which was much cheaper. It was male only, and I found it super comfy and spacious actually. It also came with onsen as well.

For urban camping, there was a spot on the west side of town near the river which was great - right next to the river so you can bath, secluded but close enough to the city. Sorry I forget all the names of the areas I stayed in, but you can find lots of info here about urban camping http://wikitravel.org/en/Urban_camping_in_Japan

Hitchhiking in Japan is also great fun if you want to consider that as well.
http://wikitravel.org/en/Hitchhiking_in_Japan