Sweet and simple: A list of supermarkets in Japan that specialize in or carry a decent selection of imported goods. We'd like to lengthen this post as we become aware of new chains, so if you have a favorite shop you'd like to share, please let us know in the comments section.
Hokkaido
Jupiter Coffee (Sapporo)
Costco (Sapporo)
Don Quijote
Tohoku
Jupiter Coffee (Aomori, Morioka, Akita, Sendai, Fukushima, Koriyama)
Don Quijote
Kanto
Jupiter Coffee (Tokyo, Yokohama, Fujisawa, Kumagaya, Kashiwa, Ichihara, Mito)
National Azabu (Tokyo)
Nissin (Tokyo)
Costco (Tokyo, Yokohama, Maebashi)
Don Quijote
Please also take a look at this
wonderful list of Tokyo shops by bento.com
Chubu/Koushinetsu
Costco (Nagoya)
Jupiter Coffee (Nagoya, Shizuoka, Numazu, Niigata, Fujiyoshida, Nagaoka)
Don Quijote
Kansai
Costco (Kyoto, Osaka, Kobe)
Jupiter Coffee (Kusatsu, Otsu, Kyoto, Osaka, Kobe, Nara)
Don Quijote
Chugoku/Shikoku
Costco (Hiroshima)
Jupiter Coffee (Okayama, Hiroshima, Sanyo-onoda, Tokushima, Takamatsu)
Don Quijote
Kyushu
Costco (Fukuoka, Kitakyushu)
Jupiter Coffee (Fukuoka, Saga)
Don Quijote
Others...
If you don't have a Costco local to you, you can get
Yoyo Market to buy from Costco and ship to you
Yamaya markets, other liquor import stores
Here is a list of Yamaya shops, too:
https://www.yamaya.jp/pages/images/2011nenmatu.pdf?category_id=83
They are quite prominent nationwide, with a great selection of imported goods. (Not just liquor!)