One of the things I like about Japan is that it's a place you can relax and not worry about tipping.
The one place I've seen it done regularly is in Ryokans, as mentioned above. My experiences have been business trips where the company paid. It seems like non business kokorozuke is paid by guests with a high social standing or a lot of money ...but even then it's not a necessity.
It's also not unusual to give a smaller anount to the furniture transport company workers who helps you when moving house.
The other situation I've seen it is when a nurse at a hospital is given an envelope after caring for a family member. My wife tells me that this is now also rarely done and a gift is given instead.
When in a hurry I sometimes round up when paying for a taxi, but this too is often refused.