I use two methods. When reading journal articles, I use a PDF library which allows me to make highlights and annotations (e.g. Mendeley, Papers). I can also cut-out good quotes and paste them into the notes section to reference later. I also tag the PDF with important information so it is really easy to come back to latern on. Of course, programs like Mendeley and Papers also work like EndNote, so you can build bibliographies as well.
More recently I have started to use mind-mapping programs (I like xMind) and I will map out key arguments, theories, and quotes from what I read. I can then connect this to other readings, or take parts of the 'map' and add it to another relevant topic. This helps when trying to make sense of complex ideas. It is a great tool for visual learners (like myself).
I have really moved away from storing notes on paper because I feel it takes too much time to retrieve the information when writing articles and papers.