Though it's largely a non-tipping society, providers of certain services may appreciate a tip, but only in yen (estimate a little more than 100 yen to the dollar):
For a tour guide, offer 2,500–5,000 yen in an envelope.

A private driver will usually expect to have you buy his lunch, around 1,000 yen.

The room attendant at a ryokan—a traditional Japanese inn—usually gets 5,000 yen for one or two nights—always in an envelope.

To tip a cabdriver, round up for a very short ride—although he may refuse the extra.

Others who may decline your offer of a tip: concierges, porters, and waiters.

Source : CNTraveler.com