French National Library in Paris have put up a part of their manuscript collection online here. Some of their Hebrew manuscripts are online as well here. Just search for “hébreu” and they will pop up.
HebrewBooks.org just announced that they opened up a new website dedicated to Hebrew manuscripts called HebrewManuscripts.org. So far they have 1000 manuscripts from the JTS library. Each manuscript can be downloaded in a convenient PDF. Unfortunately the manuscripts are scanned in 2 color, like books, and are not high resolution so some of them are either very hard or impossible to read. Hopefully they will improve the site with time and will put up color, high resolution scans. It’s a great start.