It is becoming easier to access the Islamic intellectual heritage in manuscript (although some libraries particularly private and waqfi ones still pose challenges) and online resources and digitisation are helping. India has treasure troves all over the country; the Union government is currently undertaking a massive manuscript survey to produce a Union catalogue and eventually allow digital access to the millions of codices in various languages.
Alongside the existing survey of Indian libraries in the al-Furqan World Heritage Survey edited by Geoffrey Roper, Omar Khalidi produced a document that was published in MELA Notes 72-73, Spring 2002-2003.
Two of the most important libraries recognised by the Union government's manuscripts survey are:
Raza Library in Rampur, UP - an excellent and valuable collection set in the old palace Hamid Manzil in the walled Qila area of this small old nawabi town some 180 km from Delhi. The library is run by a truly remarkable retired ASI officer Dr Waqar Siddiqui, a man of impeccable old-style Lucknowi manners. Visiting scholars can stay at the guesthouse in the adjoining Rang Mahal (the former zenana). Access does require some pestering of the librairian Dr Abu Sad Islahi but it is easy enough. Copies require permission and especially full codices require special clearance.
Khuda Bakhsh Library in Patna, Bihar - another valuable collection set in old Azimabad in Patna. The website has the catalogue in pdfs available. The director Dr Imtiaz Ahmed is very approachable and helpful and CD copies of codies can be made.
One 'clearing-house' of microfilms taken from around India is the Noor Microfilm Centre in the Khana-yi Farhang in New Delhi. Established by Dr Mehdi Khajeh-Piri, it has an enviable collection which is fully catalogued (and these catalogues are printed). I obtained some copies of works from the Azad Library at Aligarh Muslim University and from the private collection of the Raja of Mahmudabad from them earlier. The CD copies are perfectly usable - perhaps not as detailed and user-friendly as the digital CDs produced at the Suleymaniye in Istanbul but adequate with 3 folios taken as one frame.