Classical Quest kindly invited me to participate in sharing my note-taking methods along with many other WEM friends (you'll find all their links at her blog).
One of the first rules of reading with The Well-Educated Mind is note-taking - your "handshake" with the book, as Susan Wise Bauer says. She has a specific formula for note-taking which I used exclusively when I started but, over time, I have morphed into a slightly different method that still holds true to the format she lays out in the book.
The first essential is the character list. At first I thought this might be unnecessary but discovered I needed it for many of the books (especially those Russians with all their different names!) so I have faithfully continued to note each character and their relationship to other main characters in the novel. Sometimes this has been tedious - especially when reading The Portrait of a Lady. Henry James devotes the whole first chapter to the "old man" and "two other gentlemen" but we don't learn their names until the chapter is almost finished. But, more often than not, it's a very useful practice.
When I started with the first novel, Don Quixote, I faithfully made notes in the margins of the book and turned down the corners on pages that had interesting tidbits or confusing information. Sometimes I had difficulty finding a passage that I wanted to reread when I went through the questions in the first and second stages of inquiry so my notes started being transferred to the same page as my chapter summaries, making things easier to find (as long as I remembered to write down page numbers!). Now, I write the chapter summaries on the left side of a piece of white-lined paper and any notes or questions on the right side. This has been my format through many books and, now that I read many of the novels on an e-reader, it's an ingrained habit. Occasionally, I'll be out and about without my reading notebook. At those times, I usually find a piece of scrap paper and write down quick summaries and thoughts and, during my next reading time, transfer those bits to my "official" notebook (which really just consists of a pile of white-lined paper). When I finish each book and have made notes and jotted down answers to questions, all the pages get stapled together and put in a binder and I start with fresh pages for the next book.