I agree on your point about visual indexing. There's one more reason I prefer paper books - when I read a book, I take something from it, be it technical knowledge, be it "self help" type of advise. When this book is sitting there near my work desk, in a bookshelf, a small glance at it triggers back those memories and values gained, therefore I find it easier to apply the knowledge from the book, when it's constantly reminding me of it's existence. With ebooks, it would just end up somewhere hidden deep into the folder structure or in an index of some app (iBooks for example) and the memories of it slowly fade.