Just thought it might be useful to gather together some links for full digital images of manuscripts that are available online (various others are in the process of being uploaded including apparently the collection of the former Asafiyya in Hyderabad kept at the Osmania University Library and al-Azhar's collection which was partly online and has gone offline).
1) King Saud University in Riyadh - an interesting and quite mixed collection just listed in order and not divided by subject. You need to browse to find what you want but the quality of the images is excellent.
2) Princeton University Library - around 200 manuscripts so far from the Islamic collections (the best in North America) are available
3) Manuscripts from Mali - a small collection digitised and available through the Library of Congress
4) Iranian manuscripts and catalogues portal - a wonderful site with various types of links named after the great bibliographer Agha Buzurg Tihrani
5) American University of Beirut - a small collection from the Jafet Library
6) Markaz Wadud li-l-makhtutat - a clearing house allowing download of digital images
7) The Minasian Collection at UCLA - at the moment the catalogue is up but the digital images will apparently follow
Also this is a useful site run by the Islamic Manuscript Association which provides links to online catalogues.
And here are a few useful sites on manscripts:
1) Jan Just Witkam
2) Youssef Ziedan
There are surely plenty more and would appreciate any further links which I can supplement later.