Generally, see Dominik Wujastyk's collection of manuscript catalogs.
- CHENNAI: The three-volume alphabetical index of Sanskrit manuscripts in the Government Oriental Manuscripts Library, Madras.
- DELHI: IGNCA has digital copies of manuscripts from all over India, many of them Sanskrit. Full lists--divided by collection--are available here.
- Note that where IGNCA does not offer lists, usually they have digitized their microfilms of manuscripts. Their microfilm database is searchable through computers in their library
- KASHMIR: Stein’s Catalog of Sanskrit mss in the Raghunatha Temple of the Maharaja of Jammu and Kashmir.
- LAHORE: Punjab University has their catalogue online in a series of pdfs. Also note the project to digitize their collection here.
- Kasliwal's 5 Volume Rajasthan ke Jain Shastra Bhandaron ki Granth Suci (pdfs are also available here) Scroll down to title.
- Bhandarkar's Report of II Tour in search of Sanskrit Manuscripts made in Rajaputana and Central India, in 1904-5 and 1905-6.
- JODHPUR: some RORI volumes as well as a few other catalogues are available for download here.
- TAMIL NADU: Madras Government Oriental Library, many volumes here.
- OXFORD: Clauson and MacDonell's 1912 handlist of Stein's manuscripts at the Bodleian Library and Keith's List of Indian Institute Manuscripts.
- Aligarh Muslim University, Zaidi's catalogue of their Persian manuscripts on Hinduism.
- PATNA: Khuda Bakhsh offers their catalogues online, which works at least some of the time.
- RAMPUR: Raza Library's Persian manuscript catalogs from 1996-2000, volume 1, volume 2, and volume 3. (Hat tip to Owen Cornwall and Daniel Majchrowicz)
- TONK, RAJASTHAN (Hat tip to Owen Cornwall and Daniel Majchrowicz)
- CAMBRIDGE: Browne's catalogue is online here; the University Library offers links to a few other catalogs.
- EDINBURGH: 1925 catalogue of Persian and Arabic mss.
- British Library
- Royal Asiatic Society of Great Britain and Ireland: Persian manuscripts searchable online
- Wellcome Library's catalog as a pdf.
- OXFORD: Bodleian Persian Manuscript Catalogue: Vol 1 and Vol 3. Also see full list of their catalogues.
- Also note the joint project of Cambridge and Oxford to produce an online catalog of all Islamic manuscripts in the two collections.
- UNITED KINGDOM: The incomplete Fihrist catalog.
- New York: MET Museum catalog of Persian manuscripts from 1914.