十二国記 - NHKの十二国記サイト (the official Japanese site).
Twelve Kingdoms - the official United States site.
山田章博 - the official site of the artist of the Juuni Kokki novel and DVD cover illustrations, Akihiro Yamada.
Shashinboku has a very comprehensive listing of the 12k stories in chronological order, and is usually up to date regarding online translations.
The list below is also in chronological order:
Higashi no Watatsumi, Nishi no Soukai
Sea God of the East, Endless Ocean of the West translated by Otyaku. (incomplete)
Tonan no Tsubasa
The Wings of Aspiration translated by Candidat Tokolsky. (in slow progress)
Tasogare no Kishi, Akatsuki no Sora
The Shore in Twilight, the Sky in Daybreak translated by Harunako and Meici. (incomplete)
The Juuni Kokki Community's Journal - A LiveJournal 12k community where people post interesting tidbits and their art and fanfiction.
Damien's Juuni Kokki page - Links to many 12k resources and a mirror of most of the online translations out there.
Phenomenal: A Twelve Kingdoms Fansite (currently down) - A very thorough fansite with lots of information, from a glossary and youma list to in-depth character decriptions and a large gallery.
十二国記の部屋 - Essentially the ultimate 12k resource on the web (if you understand Japanese and aren't looking for images).
十二麒麟・juunikirin - Hardcore fandom. It's mostly in Japanese, but some parts are translated into English.
戴極圏 - A Tai-oriented fansite with detailed data and some fanart.
わらう太陽 うたう月 - Amusing comics, fanart, and info about 12k in Korean.
泰麒が倖せになるのを陰ながら応援する部屋 - A Taiki-oriented site. Lots of information and ramblings with many handdrawn image accompaniments.
山水の箱庭 - Fanfiction, fanart, some comics, Youko x Keiki.
落書ノ島 - Some fanart and comics.
Limelight - Some fanfiction, some fanart, very Gyousou x Taiki.
Les 12 Royaumes - A French fansite with a nice flash layout.
The Twelve Kingdoms - A forum about 12k. In Russian (which I don't speak :)
Twelve Kingdoms/Juuni Kokki - a information sub-page on 12k from Cassie's website.
JASMS 147: Juuni Kokki - in German, but it has the most complete character listing I have EVER seen, as well as some general info and term definitions.
SHASHINBOKU. the magical list o' links. - Woo, information and linkage.
The Knights' Gallery - A gallery with beautiful fanart for 12k, as well as several other anime series. An absolute must see. Their (his? her?) art is amazing.
L U N A * T I C * G A T E - In Japanese. Click on "Pict log" to see some amazing 12k fanart.
* 十二国記 * - Fanart and comics.
「十二国記」によせて - Nice fanart.
#Twelve-Kingdoms - A deviantART group to which fans post their fanart and cosplay.
Art from the anime
~ In the Land of Dreams ~ - A screenshot gallery.
EternityofPain's Gallery - A cel gallery with cel art from various episodes of Juuni Kokki.
Dragoon Adoptions - The source of the sprites on the riboku navigation tree. Many more sprites where those came from.