The British Library

http://www.bl.uk/onlinegallery/virtualbooks/index.html

Check out the Mewar Ramayana virtually reunited!

The University of Cambridge Library 

http://cudl.lib.cam.ac.uk/collections/sanskrit

Cambridge Digital Library-Sanskrit manuscripts digitation project

The Nepalese-German Manuscript Cataloguing Project (NGMCP)

http://catalogue.ngmcp.uni-hamburg.de/wiki/Main_Page

Digitized Jain manuscripts on Jainpedia

http://www.jainpedia.org/manuscripts/jainpedia-manuscripts.html

National Mission for Manuscripts (Government of India Ministry of Culture project)

https://www.namami.gov.in/

Indira Gandhi National Centre for the Arts

http://www.ignca.nic.in

(includes a resource section on manuscripts with digital copies of catalogues of manuscripts)