I'm not sure how extensive the Vatican Library's holdings are in other areas, but when it comes to old and important manuscripts of Classical Latin authors, they are second to none in the world. And now they're starting to put images of some of their manuscripts online. Their digitalization process is far from perfect -- for example, the viewer doesn't keep track of which page you're on, as many pdf viewers and other such things do. And for another example, there's an annoying copyright announcement superimposed over the image of each and every manuscript page, not the ideal place for such a thing by any means -- but I'm still not complaining, because this online collection is still stunning. And hopefully they're just getting started.
The manuscripts so far digitalized and put online for free public view so far include, to take just one example out of hundreds, Vatican Latin manuscript 3225, also known as vat lat 3225, a celebrated Latin manuscript made in the 4th or 5th century containing fragments of the works of Vergil as well as some interesting illustrations like this:
If you're into Latin manuscripts, this digitalization project of the Vatican is really something.
And far all I know it may be just as exciting for people interested in other sorts of manuscripts -- Bible manuscripts, Mayan manuscripts, what have you. You'll have to ask them.