There is a lot of sites on the Web offering long lists of links pertaining to manuscript studies. In order not to copy them we recommend you just a few of them which are good to start with.
 

• ORB Online Encyclopedia. Books and Universities: Medieval and Renaissance Book Production by Richard W. Clement

A detailed comprehensive introduction into the topic.
 

• Stanford University Library Medieval pages: Manuscripts

Paleography, codicology, history of manuscripts, bibliographies, plenty of links to manuscript collections and digitized manuscripts on-line.
 

• Hill Monastic Library: Electronic Access to Medieval Manuscripts

A list of on-line manuscript catalogues, library databases, and collections of digitized manuscripts
 

• Georgetown University's site for resources on Medieval Studies, Labyrinth

A similar list of on-line manuscript catalogues, library databases, and collections of digitized manuscripts
 

• Writing Materials & The History of Books and Printing: Some Related Links

A huge list of various links on the topic.