If you are flying into Japan on a contract you signed back at home, you've probably been offered an apartment. It's nice to have the peace of mind that you'll have a place to stay upon arrival, but a little knowledge about your options will have more of that paycheck going to what you want to do.
Your first option is to stay in a guesthouse. When I first heard the term, I pictured a lodge or hostel. They're generally more laid out like dorms, and the units may or may not have a bathroom attached. The two big companies I know of are Oakhouse and Sakura House. These are probably the best options for a few months in Nippon. There is a nonrefundable management fee if you don't catch one of their (ad) campaigns, your base rent, and then a packaged utility fee. The utility fee is usually the only overpriced component of this, but your unit is furnished. Your internet connection, however, may be strictly limited. This means that certain ports may be blocked, preventing your favorite apps and downloads.
|Oak Mansion in Futamatagawa, Yokohama - 65,000|
The total difference for me was still roughly 20,000 yen ($195). Obviously, this depends on your region and distance from the train station. I paid 65,000 ($630) for a tiny room, with a single-element burner, fridge, microwave and bathroom, utilities included. However, it was a 15 minute walk to the station, then 10 minutes away from the main hub by train.
It is worth noting that most Japanese companies pay your transportation costs, so if you don't mind standing or bringing a book, you have better control over rent.
|Programmable bath with reheat/temp/water level/timer|
|6jo (6 tatami-mat room) - roughly 12' x 9'|
You may or may not have heard that the regular process for an apartment is gift money (you basically give a month's worth of rent to the manager as a thank you,) key money (up to 6x rent, refundable), and a deposit. Basically, you'll need up to 8x the advertised monthly rent to do it the Japanese way. PLUS a guarantor, which a lot of schools don't actually do. UR cuts that down to 4 months, all refundable, minus a chunk of your deposit (less than 5% in my experience).
|Separate toilet room...if you've never, you should.|
UR helps both Japanese citizens and foreigners, though getting an agent that speaks English is tricky, even in the second largest city of Yokohama. All of the emergency information, maintenance, comes in Japanese/English manuals, though. You'll need to set up your internet, power, water and gas in Japanese.
|Kitchens, hallways - 1LDK was 85,000|
What is the tradeoff? UR is the absolute most flexible and cheapest, but your unit is bare, often without even an AC/heater or bedroom ceiling light. The furniture problem is best solved by scanning craigslist for both free furniture and 10,000-20,000 ($100-195) moving truck services. Another choice is to join the Yahoo Group [tokyofreecycle]. You’ll get lists of who is getting rid of what, and where they are giving it away. It's stressful, but if you're planning to stay in Japan longer than half a year (most contracts are a year), then this is the way to go.