[quote=rpg101]
Recently, I've been taking notes in the books I read. I underline important phrases, bracket main ideas, write notes/comments in the margins, etc. Eventually, I'll record the major stuff in a moleskin notebook and I"ll have a summarized version of the main points, helping me retain the most important/influential parts of the book. 

However, I just got a book I ordered and now I realize the biggest flaw in this system is that I don't want to mark up a book in perfect condition. 
[/quote]

get a journal and just write notes in it and cite each note on the journal. That way you still get those notes that you'd want to write in the book and still have it in its flawless condition,