Below are some frequently consulted sites.
Beethoven: Digital Archives, Beethoven-Haus Bonn
Thousands of documents relating to Beethoven's works, including manuscripts, sketches, early editions, letters, and more.
Bibliothèque nationale de France (la BnF) -- Gallica Digital Library
Digital scans of manuscripts (including music) located in the BnF.
Brahms: Brahms Digital, Brahms-Institut
Includes a number of digital facsimiles of manuscripts, including autographs, as well as images and documents related to Brahms.
Codices Electronici Ecclesiae Coloniensis
Digitized versions of the medieval holdings of the Episcopal and Cathedral Library Cologne. To switch to English, select the Optionen tab at the top of the page and click on the circle next to Englisch.
Danish National Digital Sheet Music Archive
Selected printed and manuscript music from The Royal Library in Denmark. Includes some selections from the complete Carl Nielsen edition.
Digital Image Archive of Medieval Music (DIAMM)
Provides information on all known collections of medieval polyphonic music manuscripts, as well as number of digitized facsimiles of these manuscripts. Registration is required to view images, but this is free.
Early Music Online
Includes digitized copies of 300 volumes of early printed music, made available by the British Library.
Juilliard Manuscript Collection
Collection of 128 autograph manuscripts, sketches, engravers' proofs, and first editions.
Medieval Manuscripts in Dutch Collections
Descriptions of medieval western manuscripts in Latin script and produced up to c. 1550 preserved in the Netherlands.
The Morgan Library & Museum: Music Manuscripts Online
Digitized facsimiles of manuscripts held at The Morgan Library & Museum, covering a wide range of composers.
Music Treasures Consortium
Available through the Library of Congress, this site provides access to collections from the British Library, Harvard University, the Library of Congress, Juilliard School, the Morgan Library & Museum, and New York Public Library.