I never wrote in books until I bought some used textbooks my second year in college, and in one of them someone had done an excellent job of highlighting them. Key terms were marked with a wide swath of highlighter, and the definition of those terms were marked with a narrow swath of highlighter. I noticed that the good highlighting made it much easier to find the key terms when sweeping through a section doing a review for test. Since then, I like flagging critical portions of non-fiction books, most commonly with a vertical line in the margin by the key lines, or a star. I have a few quilting books were a critical bit of information is tucked in an odd spot, and I'll make a point of circling the information and sometimes add a reference note in the area where one needs the information. I found it very liberating to realize that I can mark up my own books if I want to, after all those years in school of being admonished not to make any marks.
With library books, I will sometimes pencil in correction when there is stupid error, like the wrong there/their/they're or wrong its/it's. My grandmother was a big reader in a town with a smallish library, so she would write her initials inside the front cover of each book she read, so that she would know if she'd already read it. Eventually, she noticed the initials of several other people regularly appearing on the same page - other people were using the same method!