If you haven’t already, check out the wonderful digital publication of the Codex Sinaiticus, a manuscript of the Christian bible dating from the fourth century. Its online incarnation includes an incredibly detailed scholarly apparatus divided into five primary activities:
The process of translating the physical properties of the manuscript into digital display is documented not only through imaging standards and transcription policies, but also with a really interesting account of conservation analysis, nicely supplemented with photographs and charts. The interface is also really cool; when looking at manuscript pages, users can control what exactly gets displayed. Display options include image, translation, transcription, and physical description, and the interface changes depending on the options selected.