Paris:
In addition to the above (but not the Tour restaurant): Guy Savoy, Alain Ducasse (still - coz the room is so good) and I still like Helene Darroze.
San Sebastian:
People have mentioned Arzak; but better still is Martin Berasategui in Lasarte. Akelare is very good too.
Japan:
Tawaraya, but only if you get a good room. It makes the experience. Problem is that the nuances of kaiseki are sometimes lost on non-Japanese palates. In Tokyo for haute kaiseki ? Try Waketokuyama.