I totally agree it's mostly European libraries. I got to take a paleography class at the Vatican Museums (which I was really very lucky to get to attend) and I had been warned that the situation was bad, but Lord, it was bad. I guess they probably were only letting us put our dirty hands on the less-than-A-list stuff, but there was bright red ink on nearly every page. Almost like the book was illustrated in color.

I worked in Harvard's rare books library, the Houghton, as a very green horn. It was my work study so I wasn't paid to ask questions, but even I was alarmed by the amount of red ink, duct tape, crayon (seriously), and pen marks in some of our most beautiful manuscripts. I finally asked my boss after almost 3 years and he told me a long tale of woe about the Houghton's bad luck with a truly cray long-time director who loved the books, but beat them up in a 1950's style well after everyone else this side of the Atlantic had laid off. When he left the library they found out that he'd actually purchased a bunch of the books in his name with his own money, but using the library's invaluable reputation and connections with dealers. On his last day he packed em up and took em home. But hey, at least he willed them back.