Japan
 

Kyoto:
I recommend J-Hoppers Hostel in Kyoto.
Founded by a trans-continental motorcyclist in 2002
http://kyoto.j-hoppers.com/
Dormitory beds: JPY 2,500
Private rooms: JPY 3,000 - ¥3,500
Free parking lot for motorcycles (with a caretaker on duty for 24 hours a day)

very good place
 

yes, Chris, this is a very good place to stay in Kyoto. I can also recommend it. It is near the centre, so not far from many of the temples. And the owner (long distance biker as well) is very helpful, he helped me finding a dry place to work on my bike, which is not easy in crowded japan. greetings from Bulgaria Mika

Japan, Tokyo
 

Hello,
can you give me a tip to stay in Tokyo with the bike?
Hartmut

Try Economy Backpackers HOTEL NEW KOYO
I don't know if they have parking, but you can probably park on the street.