JAPAN
-Kyoto
--Meditation Records - large selection of ethnic music, drone, psychedelic, minimal techno. Basically all things mellow and psychedelic. I'm not sure of its newest location but when I lived there it was in a gorgeous part of Kyoto, tucked away between homes.
--Avis Records - near Shijo and Kawaramachi in the Teramachi (covered shopping alley area) - awesome, awesome selection of Japanese hardcore and metal with lots of great imports there. I bought stuff ranging from Hellchild to Deathspell Omega to SWARRRM. And reasonable prices too!
--Cafe Independent - there's a record shop in the cafe that has some noise, jazz, classical etc. Pricey as hell generally.
-Osaka
--Timebomb Records - huge selection of stuff but you can find some great obscure things tucked away in the shelves.
--Grave Records - owned by Chew of Corrupted. Nice selection of metal, hardcore, noise with good art books too.
USA
-San Francisco
--Amoeba Music - inside what used to be a bowling alley, the selection is huge and always changing. You can find some good second hand experimental records from time to time.