Manuscripts containing musical scores have been preserved online mostly by their incorporation into database projects, though there exist many individual projects and efforts to draw on multimedia sources now available.
Medieval Music Database
La Trobe University Library hosts this site, which holds an extensive database of medieval musical texts, usually accompanied by transcriptions, translations, and valuable information about the manuscripts and their relationships to similar items. Along with individual manuscript images, the site also houses four complete works (three antiphons and one gradual). This site has an excellent search function. Unfortunately the Music Dept. of La Trobe University was closed down, so updates on the database have been sporadic.
Digital Image Archive of Medieval Music
Though this archive requires brief registration, the archive is easily searched once inside and holds an enormous collection of manuscript images in high-resolution. Along with the images in this database, manuscripts are also listed that are only part of a census of items and do not have much information related to them, so in your search, be sure to specify that you would like images of manuscripts.
This web site, which I’ve introduced before, has a good search function and a decent selection of music-related manuscripts, though not many whole works. High resolution photos are available. When using the search function you may find it useful to use more specific terms (antiphon, gradual, kyrie, gloria, rather than “song” or “music”).
Stichting Musick’s Monument: Medieval Manuscripts
In words from their own site, “The Stichting Musick’s Monument produces Historical Art Productions, partly in association with scholars from the Chair of Humanities of the University of Amsterdam (UvA).Pictures, music and text are integrated: You will hear music from the same period and the same area of origin as the visual materials; these are supplemented with explanatory text. From this combination evolves something like a Gesamtkunstwerk (a total work of art), a complete new way of digital art presentation.” A very interesting project!