Bicycle Day Harmony - Photos of abandoned buildings (not quite ruins) around Sapporo (in Japanese).
BQ-E's Site - Features galleries of abandoned building photographs, among other things (in Japanese).
G-CANS - This is very weird and very wonderful colour photos of what they describe as "the worldwide biggest enormous flood-prevention facility", an incredible site found under Tokyo (in Japanese).
Goes to Ruins - Great-looking site with lots of nice pictures (including attempts at stereographs) and a word or two of English to help outsiders (in Japanese).
Hexplorer - An abandoned buildings site featuring pictures, descriptions, articles about hazards and preparation (in Japanese).
Hdoutei - Pictures of transit and abandoned buildings, including some old military installations (in Japanese).
Kazu7 - I'm not sure what this site is called, but it's a beauty. Check out the trip to a gorgeous abandoned Yokohama theme park called Dreamland (in Japanese).
Legend of Ruins - A popular abandoned buildings site, featuring "Rules of Ruins", a few words of English(!) and lots of nice photos of abandoned buildings around Japan (mainly in Japanese).
Niigata Ruins - A well-designed page featuring pictures of ruins in the Niigata area, sorted by grades from A+ to D. Some weird stuff here (in Japanese).
Photo Gallery - Pictures of abandoned factories featuring signs like "Attention! Before leaving the dredging plant, lock the crab!"
Pure Love - Pure love of abandoned buildings, military leftovers and other nice urban scenery in south Kyushu, in this case (in Japanese).
Ruin Japan - Photographs and Quicktime VR pictures of abandoned buildings, many of which are just barely standing, in Japan (in Japanese).
Ruins4U - A flash-oriented black and white photo gallery and a message board (in Japanese).
Ruins Silent - A very nice looking site, so far featuring trips to a mine, a school and some hot springs (in Japanese).
Ruins Site - I can't tell what this site is called, but it features quite a few pictures of ruins, a journal and a guestbook (in Japanese).
Ruins of Tokai - Listings, extensive photo galleries, histories and a BBS devoted to abandoned buildings in Tokai (in Japanese).
Ruins Paradise - News, trip accounts, photographs, movies and a BBS related to exploring abandoned buildings in Japan (in Japanese).
Ruin Project Version-M - Within the M-file lies information, photographs and recommended gear related to exploring abandoned buildings near Tokyo (in Japanese).
Truth * Alleyway Reverse Side School Gang Leader - There's more to this site than just a catchy name! Lots of great pictures and stories from Niigata prefecture (in Japanese).
Usiro's Site - Pictures and chatting related to industrial archaeology and rooftopping (in Japanese).
Haikyo Biyori - Very nice photography-centred site featuring some excellent pictures of abandoned buildings and advice on photography (in Japanese).
Waste King - Nicely designed site of an all-female group featuring photographs of abandoned buildings and a little bit of the ol' butsubutsu (in Japanese).
Wild Geese - Abandoned and overgrown buildings of Japan (in Japanese).
Yu-Ki's Site - Photo galleries and in-depth descriptions of Japanese ruins (in Japanese).