I’ve bought mangas from Japan using Buyee, but it’s super expensive depending on the country. As I live in Brazil, I had only two shipping methods available, but actually was only one. They don’t send packages using Japan Post, so I paid DHL or what they call Buyee Air Delivery (even though the site shows surface mail is available to Brazil) + a domestic shipping fee, and it cost me and arm and a leg. Using Buyee, you can buy new manga/novels/artbooks on honto.jp, Yahoo Auctions and Rakuten.
If you don’t mind buying secondhand manga, Rakuten has several sellers. I’ve bought a Hirunaka no Ryuusei set with 13 volumes for 1,953yen and the first three volumes of Citrus for 398yen, then paid 300 yen of buying service fee. Since I got a 5% discount coupon the day before, the total I’ve paid was US$23.90. The package arrived at the Buyee warehouse in 3 days, and then I paid DHL + domestic shipping fee to ship out my manga. Shipping costs more than the products Well, it was my first experience, now I’m looking for alternatives.
There’s Tenso, it’s not a proxy service like Buyee, you buy items on Japanese shops using their address in Japan and they ship the packages to your country. Usage fees varies depending on the country.