Remember, many scores that are within collected editions of the library-- Call numbers beginning with M2--contain early music, some in facsimile.
To locate such scores, use the advanced search in IUCAT, and enter "M2", selecting "call number" from the dropdown menu, and entering "facsimile" in a keyword box.
DIAMM (Digital Image Archive of Medieval Music)
A portal and for the study of medieval manuscripts. Lists collections and individual sources of medieval polyphonic music dating up to 1550 (plus copious information and research about them).
Répertoire des manuscrits médiévaux notés
Includes actively maintained lists of digitized medieval music manuscripts grouped by repertoire and location (starts mid-page). Part of the network Musicologie médiéval: Resources for medieval musicology and liturgy. Production of Grégofacsimil, created and administered by Dominique Gatté
Codices Electronici Sangallenses (CESG) = Digital Abbey Library of St. Gallen
Creates a digital, virtual library of the medieval codices (currently numbering 600 and growing) in the Abbey Library (Stiftsbibliothek) of St. Gallen, Switzerland, 19 of which contain musical notation.
e-codices: Virtual Manuscript Library of Switzerland
A continuously updated and expanding virtual library accessing all medieval and a selection of modern manuscripts held by 70 Swiss libraries. As of 30 May 2017, there are 1,749 manuscripts online, 78 of which contain musical notation.
Digitized collection from holdings at the British Library of over 320 volumes of 16th-century anthologies of printed music (mainly partbooks of vocal polyphony), representing ca. 10,000 musical compositions, published in Italy, Germany, France, and England. Maintained by Royal Holloway, University of London and the British Library.
RISM: online (coverage is 1600-1800) and in print in the library (music library reference section, ML113)
Search RISM to see the music manuscripts that survive all around the world. Series B volumes are particularly useful.
RISM Series B
RISM series B documents sources by topic. The volumes in series B are published by G. Henle of Munich. Series B includes (an English translation of the title appears in parentheses where necessary):