I'll share some of my favorite restaurants in Tokyo, Kyoto, and Osaka:

Tokyo:
Tempura Mikawa
Sushi Shin (Nishi-Azabu)
Sukiyabashi Jiro
Yakitori Toriyoshi (Nishi-Azabu, Akasaka Mitsuke, Ginza, Naka-Meguro)
Kikuchi Nishi-Azabu (Kaiseki counter Kappou w/one table available)
Kasumitei Matsubara Nishi-Azabu (Kaiseki counter Kappou with private dining rooms available)

Kyoto:
Gion Nanba
Gion Suetomo

Osaka:
Sfida (Italian)