Summarizing the main ideas of the material you read in your own words, as Luke advises here and elsewhere, does appear to increase retention. After experimenting with several different note-taking software programs, I've reached the conclusion that WikidPad is the best option available. I also try to write one-sentence summaries of every article and book I read, for future reference. Here a citation-management application might help. Of the ones I tried, citeulike strikes me as the most useful.