I have no problem highlighting my books from school because they all fit the stereotypical textbook defintion, which doesn't count as real book to me, because real books shouldn't be tortorous and have things like math in them.

If you get a yellow highlighter, it won't be as noticeable...and you could always make notes in a notebook and mark down the page and paragraph number, because writing in books is naughty. :P Oh yeah, they also have special highlighters for bibles (which you may have to go to a bookstore for) but that would be good if you have books which very thin pages, because it won't leak through (they are sorta crayony I believe - and I know this because I had a LOT of religious friends in highschool).