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In most cases non-Japan residents will not be able to buy from these stores, so visit proxy services to learn more about how to order from them.
1. Amazon Japan - Items can be purchased here just as on Amazon.com (which is full of fakes by the way), unless you want to buy games as those can't be sold internationally. Watch your shipping costs here, though.
2. Rakuten - Combination auction site and online shopping mall, this place offers many rarities and competitive prices.
3. Mandrake - Online store specializing in Japanese animation goods, from the cels to the toys.
4. Animate - Online shop that is the largest in Japan for animation goods.
5. e-Capcom - The official webstore of Capcom in Japan. Exclusive items and great deals.
6. Dengekiya - An online Otaku shop in Japan.
7. P-Bandai - Order goods from Bandai!
8. Suruga-Ya - Good place for Japanese games, soundtracks, etc.