I use a bookshelf. When I'm trying to remember something I read, I find the book and read it again. The advantage over taking notes, which I used to do, is that between the time I've read something and the time I'm trying to remember it, I've read lots of other things and my understanding has changed...well there's other advantages as well. I can spend time reading instead of taking notes. The book is the source and the notes are always more vague.
There are some caveats. I like physical books. I don't worry about trying to remember everything based on the realization that there won't be a test next week. I don't try to write down every idea I have as I read because I have many many ideas and the most important ones bubble up naturally from synthesis over time -- they're not little facts, they're big abstractions.
Interestingly, yesterday I was reading a technical book I bought about four or five years ago (a used copy of ANSI Common Lisp) and read a note I had written in the margin perhaps a year after buying it (I'm on Norvig's 21 day plan for learning Common Lisp, apparently). Anyway, the epiphany I'd had and written down was obvious in the text I read up to the point of the marginal note as I read it yesterday and it took me longer to understand the note than the text.
One of the good things about getting older is rereading (fiction and non-fiction) books. After a few years good books are different books when they are reread.
http://norvig.com/21-days.html