Depends on the book. If it's something I'm reading for pleasure I won't do it. I might stick a bookmark on a page if I want to remember something. I marked the crap out of The Kingdom of God is Within You. But even the last self help book I read I used Post Its to mark passages. I like to keep my books in good condition for no reason. Their best life after me is in a thrift store, they don't have a resale value to speak of. Just some weird neurotic thing I have about books being special. Except textbooks. They're the most expensive and everyone hates them because they're so expensive.
That's my issue. I feel like if I'm reading for pleasure, I should just leave the pen alone and enjoy the book. But I'm the same way, if I feel like I'm going to reread the book, I shouldn't ruin the perfect condition. I don't go to college for a month yet, so until next week I'm blissfully unaware of textbook costs.