I don't mean to be flippant, but can I suggest trying really hard to get over that hangup? I used to feel terrible for marring them, now I feel like it's not mine if it doesn't have my writing all over it. Writing in the books has been an amazing boost for my relationship with the ideas contained therein.

Commonplace-style book indexed by works you're reading. Don't really need to index further within each work, even 5-10 pages of notes per 100 pages or so isn't hard to flip through to find something, especially if you've got little drawings and such here and there to act (as a secondary function) as signposts.

Note the exact edition you've got at the beginning (so you can probably track it down again if your copy is lost/sold/destroyed/whatever) then feel free to use page numbers liberally to reference stuff you don't want to copy completely. Consider using a set format, maybe with a box around it or something, for making note of extended quotes or passages you want to refer back to in the work—something like two lines consisting of a short phrase describing it (this is just for you to recognize later, don't worry about precision or even making sense), the first few words of the quote, then a page number(s).

Use headings however they make sense to you. Chapters/sections from the book are usually all I use.

I use notebooks roughly trade paperback sized, 120-200 pages. Can usually fit a few books in each one. Keep a separate sheet or (much smaller) notebook for a global alphabetical (or whatever makes sense to you) index of the notebooks to answer "which notebook did I use for that book I read six years ago, again?" questions.

Done right you can use these, with the book itself, to do super-fast refreshers on the high points of a book. Really handy. If you want to use it for that, include very rough plot outlines and such, too, at least for fiction. Bonus: writing all that stuff helps you remember some of it unaided, too.

I use post-its, and I let some of it stick out of the page in question to serve as a bookmark for important notions. Or if I need more space I write on a separate sheet of paper that I leave in there, at the risk of losing it though.

Kindle! I never wrote in physical books either because I normally read in bed or reclined. With Kindle, I annotate like crazy.

I use index cards as bookmarks and for note-taking. Post-it's also work.

I also wrote down references to pages, paragraphs and sentences, etc. on those cards, e.g. p42p3s5.

Nowadays I just make a light x in the margins, with a pencil (so that I can erase it if I want to).