The blog Archivalia provides a list of websites displaying Islamic manuscripts from many historical periods online, including Ottoman, Safavid and Mughal works. Some are very well known, while others are lesser known but remarkable treasures. The sites have easy to use visual interfaces and reading panes. Some even allow downloading of the image files. Well worth looking at. Since it is a blog, other users have added links to the list.
The Institute of Ismaili Studies Gallery Harmony and Delicacy in Persian Book Covers at http://www.iis.ac.uk/view_article.asp?ContentID=105133.