• Indian Manuscript: http://indianmanuscripts.com/
  • A wide variety of manuscripts on a range of topics, mostly in Sanskrit. 

• Asiatic Society of Mumbai (Granth Sangeevani): https://granthsanjeevani.com/jspui/
  
  • The Society's online platform, Granth Sanjeevani, hosts approximately 2000 manuscripts in Sanskrit, Arabic, Persian, and Prakrit from various regions of India and Nepal.  Access requires membership at a cost of Rs.2400 (a little more than $30) for a one year subscription.  

• NAMAMI (https://namami.gov.in/)
  • The National Mission for Manuscripts was established in February 2003, by the Ministry of Tourism and Culture, Government of India. A unique project in its programme and mandate, the Mission seeks to unearth and preserve the vast manuscript wealth of India. India possesses an estimate of ten million manuscripts, probably the largest collection in the world. These cover a variety of themes, textures and aesthetics, scripts, languages, calligraphies, illuminations and illustrations.

• Rare Books Society of India (https://www.rarebooksocietyofindia.org/)

• The Rare Book Society of India is the first of its kind - it is a virtual space for rare book collectors and history buffs to read, discuss, rediscover and download lost books.

• World Digital Library (https://www.wdl.org/en/)

• The World Digital Library is an international digital library operated by UNESCO and the United States Library of Congress. 
• A source for manuscripts, rare books, films, maps and more in multilingual format.

• Cornell University Library (https://rare.library.cornell.edu/)

• The Division of Rare and Manuscript Collections is Cornell’s principal repository of rare books, manuscripts and archival materials in history, literature, music, the arts, science, natural history, and technology.

• Columbia University Libraries (https://library.columbia.edu/libraries/rbml.html)

• South Carolina Historical Society (https://schistory.org/)

• An architectural treasure in its own right, the South Carolina Historical Society Museum is housed in a National Historic Landmark building and features interactive exhibits on the people, places, and movements that shaped the state and nation.

•  National Digital Library of India (http://ndl.iitkgp.ac.in/ch_document/namami/0)
• Collection of nearly 6000 manuscripts on a wide range of topics, with emphasis on Sanskrit, Prakrit, and Gujarati. 

•  Cambridge Digital Library
• This online platform provides detailed descriptions of Cambridge's South Asian manuscripts as well as complete digital facsimiles for a limited number of items. The collection comprises more than 1600 manuscripts in Sanskrit, Prakrit, Pali, and Tamil written in a dozen scripts on paper, palm leaf, or birchbark. 

• Chunilal Gandhi Vidyabhavan
• A collection of more than 2500 Sanskrit manuscripts covering a wide range of traditional subjects, with particular strengths in Purāṇa, Dharmaśāstra, Nyāya, Veda, and Vyākaraṇa.
  

• Endangered Archives Programme, British Library
• The EAP facilitates the digitization of archives around the world that are in danger of destruction, neglect, or physical deterioration. South Asian manuscripts are particularly well represented, covering a wide regional and linguistic range.

• Gujarat Ayurved University
• Hundreds of manuscripts in Sanskrit, Gujarati, and Hindi, with emphasis on Āyurveda, Dhātuvāda, Tantra, and Rasaśāstra.  

•    JAINpedia
• Nearly 100 Jain manuscripts, many vividly illustrated. Languages include Sanskrit, Prakrit, Rajasthani, Gujarati, and Hindi. 

• Lalchand Research Library
• Nearly 6000 Sanskrit manuscripts focused on traditional Hindu texts. 

• Muktabodha Indological Research Institute
• A collection of more than 2600 Sanskrit manuscripts. Offerings include more than 2000 Śaiva Siddhānta texts from the French Institute of Pondicherry, as well as a substantial number of Vedic texts from the private collections of families in the temple town of Gokarna, Karnataka.

•   Myanmar Manuscript Digital Library
• An ongoing project to digitize resources from Myanmar, with emphasis on palm leaf Buddhist manuscripts composed in Pali. 

• Panjab Digital Library
• Nearly 2000 manuscripts, largely in Panjabi. 

• Penn Libraries
• Approximately 3000 manuscripts on a wide range of topics, largely in Sanskrit. See the South Asian Manuscript Collection page for more details.

•   Raghunath Temple Library
• Collection of more than 3500 Sanskrit manuscripts.

•   Royal Asiatic Society of Great Britain and Ireland
• Nearly 400 manuscripts in Sanskrit, Pali, Sinhala, Tamil, Burmese, Malayalam, Thai, and Telugu.

•  Sanskrit Manuscripts
• An assortment of more than 500 miscellaneous Sanskrit manuscripts. 

•  Uttar Pradesh Sanskrit Sansthan, Lucknow
• More than 150 Sanskrit manuscripts, with emphasis on Kashmir Śaivism. 

• Vidya Prasarak Mandal
• Small collection of 115 Sanskrit manuscripts on a variety of topics, with emphasis on Tantra, Jyotiṣa, and Vyākaraṇa. 

Reference: https://guides.library.upenn.edu/c.php?g=1006790&p=7500027