I just finished "Eats, Shoots & Leaves," laughing uproariously all the way. And all the while, by the way, scribbling like mad in the margins and in the back of the book. I enjoy shocking people who are shocked by the notion of writing in books; but, secretly, I pity them. Those who care about the matter deeply are, after all, people who care about reading & writing, but I fear they've confused the artifact for the art. I would never consider writing in a borrowed book, or a library book, but one of the reasons that I buy, rather than borrow, books is so that I have the freedom to engage in that kind of repartee with the author.
When I'm underlining and checking off and making marginal notes, I'm not (usually) trying to denote things to go back to later -- it's part of my engagement with the book in the moment of reading it. I'm talking back to the author, and I consider it a mark of respect. I paid $160 (or some such ridiculous amount) for the limited edition copy of Ulysses that I read over the summer, and I couldn't wait to put my pen to it. It was a way of saying, "This copy, suckers, is mine! And I have the right to talk back to James Joyce."
A couple of years ago, I was reading an essay by Sven Birkerts, in which he mentions his habit of putting the dates on which he's read them at the back of his books, so that when he goes back to re-read, he knows how long it's been since his previous visit. I loved the notion and have tried to do something similar ever since -- at the very least a brief note of the date and circumstances of my reading. Depending on my engagement with the book, I can end up with mini-essays: paragraphs that wouldn't fit in the margins of a particular page.
The notion that a book should be as pristine after you've read it as when you began seems foul to me. I want to wrestle it to the ground, get bloody with it, let some of my life seep into it, just as the book will seep into me. The book that I've read had better come out of the encounter looking like it's been read, dammit!
(And did you notice that, in honor of Ms. Truss, I managed to use all of the punctuation marks?)