http://hangingtogether.org/?p=337 give some information on digitization efforts in Japan.

There is are a lot of unknown digitization projects in Japan which are making works available in Western languages. Since years I am collecting these projects with special focus on rare books before 1800 at
http://wiki.netbib.de/coma/DigiMisc

But nobody takes notice of this link list and I do not know any other comparable link list available in a western language.

Here is an updated list of digital collections I know (please take into account that I cannot read Japanese)

Doshisha University
Digital archive of rare materials
http://elib.doshisha.ac.jp/english/digital/index.html
Plaese note that also the departments have rare materials in foreign languages digitized.

Gunma University
Repository (DSpace)
https://gair.media.gunma-u.ac.jp/dspace/index.jsp
Some works (browse by date, oldest first)

Hitotsubashi University
The Burt Franklin Collection
http://hermes-ir.lib.hit-u.ac.jp/da/handle/123456789/19
Works in French.

Keio University
Treasures
http://www.humi.keio.ac.jp/treasures/
Only Gutenberg bible and Gesner's Thierbuch complete online
- Repository
http://koara-a.lib.keio.ac.jp/xoonips/modules/xoonips/listitem.php?index_id=3228
4 Kulmus works

Kyoto University
http://repository.kulib.kyoto-u.ac.jp/dspace/handle/2433/14/browse-title?starts_with=A
Some rare books.

Kyushu University
http://www.lib.kyushu-u.ac.jp/db/local/?skinid=11
It seems that only the Grotius is complete online.

Osaka City University
http://libweb.media.osaka-cu.ac.jp/els-e.html
400+ books! See
http://archiv.twoday.net/stories/4263195/ (in German)

Toin University
Savigny Library
http://savigny.toin.ac.jp/
Some rare books, see
http://archiv.twoday.net/stories/3424602/ (in German)

University of Tokyo
Books of Mori Ogei
http://rarebook.dl.itc.u-tokyo.ac.jp/ogai/foreign.html
The books are not completely digitized but unfortunately only the pages with Ogei marginalia.

Center for Research on Pictorial Cultural Resources, University Tokyo
http://www.picure.l.u-tokyo.ac.jp/theme/index_j.html
http://www.picure.l.u-tokyo.ac.jp/sitemap/index_e.html
Image databases (Piranesi etc). Links of the English version don't work.

Digital Archive of Toyo Bunko Rare Books
http://dsr.nii.ac.jp/toyobunko/
Some works.

Tokyo University of Foreign Studies
C-DATS Digital Library
http://www.dilins.c-dats.tufs.ac.jp/da_lists/full_images.html
http://repository.tufs.ac.jp/handle/10108/29
Including at least one work before 1800

Tsukuba University
Digital Collections - Rare Books
http://www.tulips.tsukuba.ac.jp/pub/tree/kichosho.eng.html
Large (hundreds of books)
Click on this sign to see the digital books.

Waseda University
CLASSICS
Search the OPAC, e.g.
http://wine.wul.waseda.ac.jp/search/X?SEARCH=jap*&l=&m=v&searchscope=12&Da=&Db=&SORT=D

There might be some other stuff I don't know!