How can I annotate my books?

I'm having trouble finding the answer to this question. Throughout all the books I've read, I have always wanted to scribble notes and jot down ideas in the margins. However, I think this is defacing the book, and makes it incredibly harder to read a second time through.

I'm considering adopting ebooks because of this conundrum. I've heard things about annotating in Kindle books (how the annotations are indexed and displayed on one page, the ease of annotating) but I really, really, REALLY, dislike the virtual-ness of them. I like holding a hefty stack of pages in my hand, flipping the pages as I become engrossed in the text. Ebooks just can't do that.

Should I have two copies of my books -- one physical, to read, and one electronic, to annotate -- to satisfy both desires? That would certainly become hassle-some, and switching between paper and electrons would certainly break my concentration.

I know it's probably silly to think this deep into the problem (I've been researching it for the past three hours, including posting to AskReddit) but my books are extremely valuable to me. My fear is that an easy solution doesn't exist.