Some companies pay for one round-trip per year to the U.S., do they include that?
I absolutely wouldn't go unless they pay for a relocation service in Japan to help you find a house and file ALL necessary work and residency permits, etc, because you don't want to try to do that on your own.
What do they pay for moving and/or relocation expenses?
Do they include any kind of a relocation "bonus" to cover incidentals and get you through to your first paycheck?
If for whatever reason you need to return home before the end of your contract, how much will you need to reimburse the company?
Make sure they pay for your flights there and your flights home at the end of the contract.
If you have kids, check to see how much they will pay to have your kids attend an international (i.e. English-speaking) school.

I've been to a fair number of foreign countries for business, and to me, Japan seemed like it would be one of the hardest places to be an expat, just because things were very different than a "Western" culture/lifestyle, and very few people spoke English. I have friends who have lived there and absolutely loved it, but they were in the military, and being a military expat is different than being a regular expat.