The Difference between Archives and Manuscripts
Because I am a librarian, I believe that those who search should find. Someone was led to this site today after having used the search string "difference between archives and manuscripts."
I don't know who the searcher was, but if he or she feels kinda like Bono did back in 1987, (i.e. I still haven't found what I'm looking for,) then I have some good news.
A Glossary for Archivists, Manuscript Curators, and Records Managers (The Society of American Archivists, 1992), edited by Lewis J. Bellardo and Lynn Lady Bellardo, defines archives as "The non-current records of an organization or institution preserved because of their continuing value." It also defines manuscript as "A handwritten or typed document."
The University of Maryland also describes the differences between archives and manuscripts in this FAQ.
Personally, I think that the difference between the two lies in who created the documents and why they were created. If documents were created by an organization, institution, business, agency, or individual for legal obligations or business transactions, they are archives. If they were created or collected by individuals or families for reasons other than these, they are manuscripts.
There is some ambiguity inherent in the way I view the distinction. For example, personal papers (i.e. a type of manuscript collection) often contain information about business transations such as land purchases, stocks, and investments. But these series within the overall collection are generally small portions of the overall collection and do not represent the character of the whole. Still, I think that evaluating the character and function of records generally yields a pretty clear distinction between these two types of collections.