I'm not sure which Japanese movies you're referring to. But apart from that (assuming you're staying, or going to stay in Amsterdam and you're not looking for Amsterdam based on-line DVD stores), I would suggest Fame in the Kalverstraat (near the Dam), or any Free Record Shop (there's one in the same Kalverstraat, at the other end near the Munt). Furthermore, the Media Markt (close to the Arena stadium) has a huge collection of DVDs and is not extremely pricy. They often have bargains as well.
Good luck!
Cees
PS, I'm moving this thread to the "Regional DVD Area" (non-R1). C.