My system for book notes is too keep them separate from the book. I can't really bear to write on the book. I'm OC that way. So what i usually do is either write on a separate notebook (this is where my handbound notebooks come in handy!) or write them on small index cards and insert them into the books. When I write on my notebooks, I would also note the page and book which triggered the flurry of ideas and thoughts. That way, I'd know where to look when I need to read the original passage. :)

I had an English prof who said the problem with writing on the book itself is that you define a certain "path" through the book, a certain understanding. And perhaps the next time you read that book you'll want to approach it from a different perspective. So she used coloured sticky notes (PostIt Notes?).

I end up writing in my books anyway since I never seem to have sticky notes on hand, but I try to do it in pencil so I can erase them years later when I reread a book and feel embarrassed about some idiotic note I made the first time I read it.

I've been using Orgmode in general a lot recently (especially the capture mode for quick notes/reminders while I'm thinking of them), but I haven't tried using it for book notes.

The problem with that, and with using a separate notebook, is that then the notes are separate from the book itself (which provides the context for the notes). So I dunno.

@BeSlayed reminded me of something. Recently I also use a free Android app called Catch Notes. I take a picture of a book's page, and attach that to my note where all my thoughts are written in. :)

This is scary.... I just bought Seth Godin's Linchpin for my Kindle and was just thinking about how I should keep notes while reading. The Kindle has the feature to highlight phrases and write notes which you can then export but the keyboard is a little cumbersome to type on in my opinion.

I think it would nice to share my notes which means keeping them digital but I am not exactly feeling sitting by my computer while reading a book ya know? So maybe its going to be a mix of writing by hand in a notebook then transcribing the "highlights"

Charo: I note quotes and page numbers, too. It's satisfying being able to go to the right point in the book. I usually note ISBNs, and if I'm diligent, I also do edition numbers, as sometimes versions repaginate.

BeSlayed: Excellent point about fresh rereadings! I don't think it's a problem to recreate the context for the notes, though, either through quotations or page references. It's a good way of checking if you understood enough and captured enough in your notes, actually. When I can't remember why I made a cryptic note about page 32, it's probably time to review the book and flesh my notes out further.

Charo: There's an interesting workflow there. I should try that. I've also tried dictating my notes, which is handy because it helps me get Dragon NaturallySpeaking used to my diction, too.

Travis: You can also keep paper notes (with sketches! ;) ) and then scan them in or take pictures of them. =)

I also have used the Kindle notes and highlighting. I thought it worked quite well on a personal level, but doesn't work well with book groups. Everyone else uses page numbers and Kindle uses line numbers. "I really liked what was on line 10,213" doesn't go over well.

The nice thing about the Kindle highlighting is you can also enable it to see what others have highlighted.

And yes you can dump your mark up file to the computer and open it in a text editor and add more notes and thoughts as you read through them again.

No ready made answer.
How about using Evernote (heard of that via lifehacker)
& ask your question to the lifehacking community
en.wikipedia.org/wiki/Evernote

I read on the Kindle, which has highlighting capability. Makes it very easy to go back to the places you've highlighted. It also has a feature that will let you know what others have highlighted in their books. Sort of a "crowdsourcing" of key ideas. Very cool.

@Sonja: I have been using Evernote but probably not to the fullest of its ability. I know some pour practically everything into it but I mainly have notes about various projects in it. Great for adding a quick not via the Evernote App on my Droid. Never thought of using it for a book notes though...

Google Books has some features for creating either public or private virtual bookshelves, and for annotating books you've read. You may want to check this out.

Update on book notes: I posted more of my book notes online. =)

When I am reading a book it is usually on the train (to and from my office) and the book is usually a library book.

I use a slip of paper as a bookmark and I write my notes on this paper. When I have finished the book, I scan these pages. Sometimes I take note of important pages in the book for scanning
but I try to restrict the number of pages to scan as it takes a reasonable amount of time.

Sometimes I realise the book is so good, that i decided to buy my own copy, then I head over to bookdepository.co.uk or abebooks.com!

Charles

I like mindmapping software for keeping track of my book notes. Xmind is currently my favourite.
http://www.xmind.net/
It's free and runs on Linux and the other two OS'es as well.

You can really see relationships between books when the connections are visual [ with your notes too, of course ]. But mindmapping software isn't quite at the level it needs to be to fit everyone's needs.

I enjoyed the post and the comments here, as well.

Sorry, a little late with my reply. Someone mentioned index cards. How about sticky (post-it) notes that you stick at the top of the page, on the blank space, so no printed word is harmed in case you want to pull out the note later?

Kevin: I'm pretty happy with Freemind as a graphical mindmapping tool. On the Android, I can edit mindmaps using Thinking Space, which reads and writes Freemind mindmaps (and can sync through Dropbox).

Chet: Might be handy. I've tried Post-it flags and metal book darts before, but a larger Post-it note might be good because I can write notes on it. Hmmm...

Aha! Emacs has a freemind.el package. I should have known... : )
And runs on Android, too. I am checking it out now.

Sacha can you put your drawings as images into either Emacs org mode or Freemind?

Sometimes, a picture in a note really IS worth a thousand words.

For some time I have marked books with a sort of inverted emacs outline system - a discrete marginal dot, with multiple dots denoting higher importance. It is unintrusive unless you are scanning for them, and easily erased if the book is on loan.

I am horrible about taking notes, whether reading or listening to a lecture/presentation. I tried a few of the standard issue note-taking methods when I was in school and found that they always distracted me and detracted from my retention and understanding of the material. However, a method that I found most compelling implement was one laid out in an Evelyn Wood speed reading book. It outlined a method in which you make a mind map prior to actually reading anything, using the headings as branches and making notes under them. This method would lend itself well to translation into org mode, and once in org mode, it would be trivial to add @quote tags and put page numbers in drawers (or whatever).

Of course, I haven't implemented this with any books, so I don't know how effective it is. This is the only note-taking system that has sounded as though it would be feasible for me to use, and the most useful afterward.