Amazon.com Japan
I haven't actually ordered from their Japan site, but they do ship internationally. I mainly use them as a reference for new books and their ISBNs. Be sure to search in katakana.
Good's Land Dragon Quest Store
THE place to drool over DraQue merchandise. They don't ship internationally, though, so all you can do is drool. ;_;
Jamall.com
This is an excellent site with outstanding customer service. Two problems with them: They don't have pictures of most of their books, and it doesn't list if it is not available. Still, you can always try to order and see what happens... just try to order very current books.
Yahoo! Japan Shopping
This is another good reference site for finding out about recent DQ books.
Yahoo! Japan Auctions
The famous YJ!A. Has pretty much everything a person could ever want game-related, but you need to have a lot of money, know someone who lives in Japan, or pay extra to go through a middleman. They no longer accept international bidders unless you have a Japanese bank account.
National Console Support, Inc.
An American company run by gamers, for gamers. Their prices are more then reasonable. They currently have available Dragon Quest VII and IV (for PSX) and 10 different Dragon Quest Monsters keychain plushies. They even have the Final Fantasy cold casts and lots of other anime/game toys.
CD Japan
Great source of Japanese music of all kinds, and best of all - they ship outside Japan!
GameMusic.com
Video game soundtracks galore, plus books, DVDs, and toys. They are located in the United States.
Cyan's Dragon Quest art
I adore his fan art. He specializes in Alena, and his skills are truly extraordinary.
Astro Boys Doujinshi Circle
Lists the various anime and video game-based doujinshi published by Astro Boys.
Enix of Japan's Dragon Quest
Beautiful graphics, easy-to-navigate interface... and a current focus on Dragon Quest IV. Need I say more?
Enix of Japan
Enix of Japan's company site, the place to check for the latest info on all their games.
Enix North America
The official site of Enix, and therefore a great source of Dragon Warrior release information.
Kamui Fujiwara
Official page of artist Kamui Fujiwara, illustrator of the Emblem of Roto manga and the on-going Dragon Quest VII manga series.
Koichi Sugiyama
Yes, this is the page of Koichi Sugiyama, brilliant composer of every Dragon Quest game. His page contains info on upcoming concerts, his discography, and even information about his vintage Japanese camera collection.
Sony Japan: Dragon Quest CDs
Sony releases all Dragon Quest CDs, and this page includes past and future releases and track lists. Check here and know what to order from CD Japan!
DQ-DW dictionary
This is an EXCELLENT list comparing the Dragon Warrior location/people names to Dragon Quest's kana.
Chrissy's Dragon Quest page
Very well-rounded site with translation information for Emblem of Roto and even Dra Que 4Koma manga. If you collect DQ books and cannot read Japanese (like me), this is an excellent site to bookmark.
Dragon-Warrior.com
Just about the most established Dragon Warrior source on the internet.
DQ Shrine
A fantastic shrine to DQ (unrelated to the Slime Shrine) that has even been recognized by Enix. I love their innovative site design. *_*
Dragon Quest News Network
It's just what the title says, and it's up-to-date information, too!
National Slime Council
The name says it all!