Ancient Manuscripts from the Desert Libraries of Timbuktu.
From the Library of Congress exhibit, these scanned, original manuscripts date from the sixteenth to eighteenth century. They are indicative of the high level of civilization attained by West Africans during the Middle Ages. Manuscripts include poetry, law, Islam, science, math, and more.

Catalogue of Digitized Medieval Manuscripts.
From UCLA, you can also browse the Catalogue by the location of an archive or library, the shelfmark of an item, by the author of a text (where that information is available), or by the language of a text (again, where available).

Codex Sinaiticus.
A manuscript of the Christian Bible written in the middle of the fourth century, contains the earliest complete copy of the Christian New Testament. The significance of Codex Sinaiticus for the reconstruction of the Christian Bible's original text, the history of the Bible and the history of Western book-making is immense.

Early Manuscripts at Oxford University.
The online collection includes ancient papyri, Celtic manuscripts and other medieval manuscripts ranging from the 9th to the 16th centuries. Beginning with collections of Celtic manuscripts of Irish, Welsh, Cornish and Breton origin, the project now includes a broader range of items, dating from the 9th to the 16th centuries and of various origins.

John Rylands University Medieval Collection.
The collections include exquisite medieval illuminated manuscripts, examples of the earliest forms of European printing including the Gutenberg Bible, as well as the personal papers of distinguished historical figures including Elizabeth Gaskell, John Dalton and John Wesley. (You must have popups enabled in order to view the manuscripts.)

Karpeles Manuscript Library.
Claims to preserve the largest private collection of original Manuscripts in the world. Some manuscripts are equipped with an interactive tool enabling the user to view the document's transcription. Look for the triangle near the top left of the manuscript and drag it toward the bottom right to reveal the transcription. Documents include the original proposal draft of The Bill of Rights, the Emancipation Proclamation, the final Declaration of Allegiance Treaty signed by every Indian tribe in the United States, and more, including scientific, musical, religious, and literary works.

Leaves of Gold.
Treasures of manuscript illumination from Philadelphia collections. Includes more than 7,000 medieval and Renaissance miniature paintings showing religious scenes, classical tales, historical events, and medieval romances.

Turning The Pages Online.
The National Library of Medicine, in collaboration with the British Library, presents books from their historic collection in the biomedical sciences. This site uses advanced 3D computer generated imagery, digital image enhancement, animation, illumination models and software programming to simulate the act of easily flipping through virtual books. There is extra information about the authors of the books and the subject matter in the form of curators' notes, captions and 'tales.' You can also magnify sections of books and print individual pages.