It's a way of marking not just the words on the page, but the moment of discovery itself.
Sometimes, when I'm in a certain pensive mood, a hankering-after-something mood, I visit my old dog-ears. I'll pick a book off the shelf and flip through the pages, stopping at all the dog-eared pages. Often I can't remember what or why I dog-eared. Those are the times I wish I was not only a dog-earer, but an underliner or even a highlighter.