RISM online catalog
RISM offers you the ability to search for music in manuscript or facsimile form, and you can limit results to music digitally available.
Digital Scores and Libretti (Harvard University)
Rare or unique scores and libretti from the collections Harvard's Loeb Music Library, including first and early editions and manuscript copies of music from the 18th-early 20th centuries. As of 17 October 2017, contains over 945 titles.
The Juilliard Manuscript Collection
Digital image collection of 140 autograph manuscripts, sketches, engraver's proofs, and first editions of works by Mozart, Beethoven, Stravinsky, Debussy, Britten, Mahler, and many others.
The Morgan Library & Museum: Music Manuscripts Online
Digital facsimiles of the extensive collection of music manuscripts owned by the Morgan, including works by Bach, Beethoven, Brahms, Chopin, Debussy, Fauré, Haydn, Liszt, Mahler, Massenet, Mendelssohn, Mozart, Puccini, Schubert, Schumann, and many others.
Austrian National Library: Digital Resources, Music Prints & Manuscripts
Digitized scores in the Österreichische Nationalbibliothek (ÖNB). Truncated keyword ("any") search on "musik*"(Alle Felder) limited to Digital (Digitale Ressourcen) refined by combined mediums "Music print" (Musikdruck) and "Music manuscripts" (Musikhandschrift).
MDZ (Münchener DigitalisierungsZentrum) Digitale Bibliothek: Musikalien (Notendrucke) / Scores
Targeted retrieval of over 20,700 digitized scores from the Bayerische Staatsbibliothek (Bavarian State Library). Note the English interface poorly translates this collection as "Music supplies (notes)." For digitized music manuscripts and specifically grouped prints, scroll through the MDZ's themed collections of digitized music scores (print and manuscript), librettos, and books on music. The Munich DigitiZation Center (MDZ) handles the digitization and online publication of the cultural heritage preserved by the Bavarian State Library and other institutions.
Saxon State and University Library Dresden (SLUB): Digital Music Collections of the SLUB
Digitized manuscript and printed scores from the Sächsische Landesbibliothek – Staats- und Universitätsbibliothek Dresden (scroll down for results list of +8,760 entries). Link includes manuscripts ("Strukturtyp: Handschrift") and published scores ("Strukturtyp: Monographie") mixed with textual materials. See also SLUB's Music Collections webpage for links to themed digital collections
Staatsbibliothek zu Berlin - Preußischer Kulturbesitz: Digitalisierte Sammlungen: Musiknoten
Use the left sidebar to explore 12 categories of music scores--including manuscripts ("Musikhandschriften") and imprints ("Musikdrucke")--in the digitized collections of the Berlin State Library.
Gallica: Manuscrits musique
Links to manuscripts with musical notation and also to treatises and materials related to music (composer letters, etc.)
Index to Opera and Ballet Sources Online
Searchable online index of primary sources related to operas and ballets housed at institutions around the world.
British Library Online Gallery
Digital gallery containing images of thousands of items from the British Library's collections.
Digital collection by the University of Southampton consisting of "eighteen printed and manuscript music books owned by members of the Austen family, including the writer Jane Austen, in the eighteenth and early nineteenth centuries."
Online archive containing millions of digitized and digital items in a wide variety of formats.
You can perform a search as simple as entering "music" in the description field, then, limiting your results by selecting Media type: images, then, adjusting year of publication/coverage.