Digital Scriptorium contains a substantial database of digitized manuscripts from a score of American university collections, including Rutgers.
E-codices: Virtual Manuscript Library of Switzerland -- A growing virtual collection of hundreds of medieval manuscripts housed in Swiss repositories.
The Web site Early Manuscripts at Oxford University provides access to digital images of over 80 medieval manuscripts.
The images produced by the ongoing digitization project of the medieval library of the Abbey of St. Gallen in Switzerland are available online.
The medieval codices of the Diocese of Cologne are available online.
Roman de la Rose is a joint digital project based of Johns Hopkins University and the Bibliothèque Nationale de France.
Here are three gateways to other digitized manuscripts online: the Medieval Manuscripts on the Web page of the Syracuse University Library, the Web page of the same title by Prof. Siân Echard of the University of British Columbia, and the Manuscripts page of the Labyrinth Web site at Georgetown University.