How do you writers collect your thoughts?

I use index cards to list a few key words for future project ideas (characters, settings, plot points, etc...) I carry 3 x 5 cards with me in case an idea comes up while out and about. If I'm making a decision on plot points I categorize the index cards by pro and con or story potentiality, this can be considered critical thinking I guess. I also plot my stories scene by scene using a cork board and index cards utilizing different colored cards for subplots, themes and such. I suppose you could use the cork board in a similar manner for something like the Ben Franklin pro and con (pro on the right side, con on the left) analysis of ideas or the spider web of causality using yarn for connections.