Programming talent: The yen is super strong right now, so what looked cheap a year ago ain't so cheap now. But even if you take this into account, Japan dev salaries are lower than the Bay Area. Healthcare/insurance costs are also much lower given Japan's national health system. I know one senior/CTO level developer who was happy to come here and work for a Japanese company for almost 1/2 the salary and one of the reasons why he was happy with it was the healthcare cost reduction for his family.

Fixed costs: Office rent — You must get used to having a smaller space to move around in than some of the cavernous office spaces that (successful) SFO startups enjoy. But all in all value for money is roughly similar to other big cities. As a guide, we pay about US$3,000/month for a 700sq ft office w/kitchen/bathroom etc.

Travel etc except for cabs is cheaper I think.

Food is, hmm. Well you can eat for really cheap, or you can blow all your dough on one meal. Up to you.

Utilities etc — probably the same as anywhere else.

Hosting, accounting, whatever — As you might have seen (http://hackerne.ws/item?id=2115203) we use a whole bunch of US services for this stuff. We pay about $400/month for our accountant.