There are many digitised manuscripts available through universities and libraries. Here are a few that I have been told about-
The Yemen Manuscript Digitization Initiative– This is a combined project with Princeton Uni & Free University, Berlin. They have been digitising Yemeni manuscripts from private libraries and making them public.
The Islamic Manuscripts Collection at the University of Michigan. There are catalogue details, as well as some pictures up in the Hathi Trust Digital Library, which is where the images of the manuscripts can be located.
The Walters Art Museum– the Digital Walters. Not only are their Persian, Ottoman and Arabic manuscripts but also many European manuscripts.
Vivarium– The Hill Museum & Manuscript Library. This is the digitised collection from Saint John’s Abbey and University. This also includes their coloured microfiche collection.
MENALIB– The Middle East Virtual Library. This is run by State and University Library Saxony-Anhalt in Halle, Germany.
Chester Beatty Library has an interactive seal collection. If you know how to decipher seals, they are looking for your input!
Finally, for those wishing to learn Middle Eastern calligraphy, Calligraphy Qalam shows beginners how to do Arabic, Persian and Ottoman calligraphy.