In Japan the toilet may or may not be connected to the bath. If they're together, it's called a "unit bath".
Another thing to check for is the hot water. Is it always on, or do you have to turn it on manually every time you need it?
Apartments closer to train stations tend to be more expensive. If you get a bicycle, you can often find a cheaper room withing biking distance.
Going through an agency is usually a good idea. This one took good care of me. You'll need to find someone to help you if you don't read Japanese, however.
アパマンショップ不動産ポータル [賃貸物件,マンスリー物件,売買物件,投資物件,会社情報]
Contracts are generally for two years, although you can find monthly (and possibly other) if you want.
Unless you go to a place like LeoPalace, the apartment will be furnished with next to nothing. My apartment came with walls and lightbulbs in only the toilet and bath areas.
Here is an open apartment in the building I used to live in.
http://www.apamanshop.com/detail/20110411010820/
The "6.0" you see in the rooms refer to their size. 6.0 is the standard size room.
If you have any other specific questions, ask away!
You know, the more I look at it, I think that is the room I had. 2nd floor, corner apartment, the layout, etc. Oddly enough, that red car in the picture looks eerily like my old car!