I'll put in a good word for hostels too. Japan's hostels, compared to hostels in other countries, are extremely clean and quite affordable (stayed at 5 over the course of 3 weeks and no complaints). I never had any iffy experiences in one, and I met most of the people I hung out with on my trip in them. I stayed in one in Germany that was definitly not up to Japan's standards, but was still fine. Here's the room at Tokyo Yoyogi I stayed at. The nice thing was that all rooms are individual, and it's only 30$ a night with a hotel membership:
And I'll share my Japan pictures experience too if anyone wants to see! Complete with witty captions:
http://www.geocities.com/corybobory/ ----> Japan Pictures
And someone mentioned writig down the place names in kanji as well. This was a good idea and I did this too (partly to learn the characters). It helped and was fun to be able to read them, though most of the place names were in romaji as well except on the rural busses in Kyoto, which I didn't write down... but I recognized one character and that got me through haha!
P.S. Did anyone else find pillows in Japan were like bean bags? lol I found them quite uncomfortable...