The same monastery that sponsored the greatest work of illumination of at least the last two centuries, the 
St. John's Bible, has put a large selection of their manuscript collection 
online.  In many cases the images are not as high-quality as I'd like and the search engine is a bit odd, but the breadth of the collection more than makes up for it. It includes:
I was first attracted to the site because the 
Hill Museum has the ability to search for illustrated capitol letters by letter, and I was hoping to build a new banner:
(letters from a 13th C Homillary 
A and 
M)

(letters from a 13th C Latin "
Vitae sanctorum" [a 16. Februarii usque ad 31. Martii].A and 
M)

From another part of the world, both then and now, the 
Walters Art Museum has started digitizing it's 
Arabic manuscript collection.  This example of 
Kufic is a tiny crop of the full-screen image available

A