Here is a selection of trusted online stores specializing in Anime and Japanese products.

AmiAmi
CDJapan
Hobby Link Japan
Hobby Search
Hobby Stock
J-List
Japan Trend Shop
Kid Nemo Company
Otacute
Play-Asia
Strapya

The following websites provide proxy services for shopping from Japanese online stores (including Amazon.co.jp) that only ship within Japan.

Goody-Japan
Japan To Door
Rinkya
Tenso