I feel like books are a conversation between author and reader, so I'm happy to conduct that conversation in the margins. When I go back it's interesting to see what I thought the last time I read it - so it becomes a conversation with a past me, too. I love finding marginalia, it brings a books previous lives, well, to life. Of course, I make a distinction between good first editions and reading copies. The FE's get cosseted in archival wrapping and kept out the sun - the reading copies get annotated.
I tend never to write in my books, of any sort (I don't have cookbooks). If I am studying for a class I will, but to me that is not a permanent book, it's a study guide. My books get wear, spine issues and such as I love them and use them, but I don't write in them, nor dog ear them - I want my books to last my lifetime, and more if possible, so I tend to try and treat them gently, but I do not idolize them in untouched form.
In my early days of AD&D, I recall that my friends and I would cross out any unique creatures in the Monster Manual once we had defeated them. We'd work our way through the archdevils and demon lords. Then we got Deities and Demigods and continued the tradition. More recently, I don't usually write in gamebooks, though I often fill them with post-it notes, mostly as bookmarks to different sections, or to note things I want to change.
Though, when I buy RPGs for the middle school that I work at, we scrawl right on the covers with big silver sharpie: