So, I've been journaling in various notebooks and blank books since I met the characters in my novel Seven Days, in August of 2006. I love to find pretty journals on sale and have quite a collection. While I started on index cards, the journals work better for me. I label my entry as to which book the scene would go in or which character it involves with a circled number at the top. I record information from magazine articles, quotes, interesting blog or Facebook posts or overheard scraps of conversation. I've recorded passages of novels or dialog I loved and the titles of interesting songs or books I "need" to look for.
When I was finishing Seven Days, I went through the journals and flagged the bits I needed to include. At first, I color coded, with different markers for each of the four books. As there were almost thirty journals to go through, it was getting stupid, so I focused on entries I wanted to use for the first book. I rediscovered many wonderful things I'd forgotten about Will and Elizabeth and their flock of secondary characters. I also discovered some repetitious dreck! As I inserted some things and cut others, I was careful to keep a file of the good stuff I'd cut, Just In Case it could be used later on in another area/book.
But, I have almost a whole shelf of the cherry wood bookcase from Mom and Dad's house filled with these notebooks and journals. I keep one in my purse, one by where I sit in the living room and one in the upstairs bathroom to capture those late night and early morning thoughts. I save my drafts and notes that I've gotten on the computer on flash (thumb) drives and keep at least one current one locked in a fire safe. Paranoia is my middle name. I still have a lot of work to do, but it's a system that works for me. What works for you?