On the Virginia Quarterly Review blog, Megan Alix Fishmann writes about the marginalia in print books that will be lost and impossible to recreate in e-books. Sure, the Kindle lets you take notes, which is nice in a dry, academic, I'll-need-this-for-my-research kind of way, but it lacks the personal touch of an inscription to a loved one.
I've never been a big scribbler in my books beyond underlining a few choice passages here and there, but that's mostly because I have a thing about neatness. When I do make notes though, I always remember where they were and can recall them much easier than separate notes stored on the computer. The visual memory of the handwriting on the page, how I happened to abbreviate certain words to make them fit, the kind of arrow or bracket I drew to frame the important parts, make a much more permanent reference point in my brain than a disconnected, elaborate filing and tagging system on the computer. Taking notes on a computer is a surefire way for me to never refer to them again.
For more of the odd and wonderful things that Fishmann writes about finding in books, you should also check out Forgotten Bookmarks, an entire site run by an employee at a rare and used bookstore about the notes and ephemera left behind in books.
(image from Forgotten Bookmarks)