I make annotation all the time- a book well-worn is a book well-loved. Shares a piece of history with me. As long as it's not comments like "about time this essay ended, how boring" and with the notable exception of library books (I'd get medieval on them, which is kind of ironic given that mostl of them
are books of medieval history), I underline (mostly with pencils- also, keep a lot of pencils around because I don't want to interrupt the reading because they need to be sharpened), I write, I put bits of reference and so on. Don't feel as if it's defacing: it's enriching.
(just my two cents, eh
)