Four categories of cards:
Yellow cards: Inspiration from others; an idea, a design, a detail or a concept I’ve come across somewhere, that somehow is relevant for my process –indirectly or directly. See for example the cards "The Confessional", "Sonder", or "The Knitting Clock".
Red: Personal reflections on process. Paradoxes, questions to myself, epiphanies.
Green: My own ideas for designs and smaller features of design. This can also be ideas developed in corporation with student assistents working on my topic.
Blue: Research discussing design concepts in some way. For research I normally keep track of it in Mendeley - a reference tool software, so this category is mostly for research that is related to visual stuff or design.
IDEO Method cards
I used the IDEO Method cards during my Master degree, and really like how IDEO works and how they make their methods accessible to everyone. This is a deck of cards with a design method on each one, and tips on how to use it in projects. And these are really not just useful for designers. They are divided into the categories Ask, Watch, Learn and Try. http://www.ideo.com/work/method-cards (they also exist as an app)
Touchpoint cards
Simon has also written an article on the use of a card-based toolkit in service design: "The card-based approach offers a tangibility that teams find useful, and that offers multiple usage alternatives."
[Clatworthy, S.(2011). Service innovation through touch-points: Development of an innovation toolkit for the first stages of new service development. International Journal of Design, 5(2), 15–28.]