I haven't found a definitive solution to this either. My current approach depends on whether I'm reading the material in connection with a particular project, or as general continuing education.
If I'm reading for a particular project, I either take notes (if I don't own the book) or annotate (if I do) as I read. Later, I'll do a mindmap for the project which contains brief summaries of the key points in my notes. After the project is over, the mindmap serves as a summary of the information and an index of primary sources.
For general reading, I take brief notes summarizing things that strike me as important, identifying possible action items, etc. These go into my Inbox and thence into my GTD system. Non-actionable items like snippets of information go into a personal wiki (WikidPad, to be precise) . I experimented with doing mindmaps of general reading -- which Buzan recommends in his book -- but decided it was too much work for not enough benefit. If/when I do want to recover the information, the snippets I saved will give me enough information to go back to the primary source if desired.
Long term projects -- learning a language, book-length writing -- tend to accumulate many more materials and require much more organization. For those, I tend to do much more organizing as I go, for instance by constructing intermediate mindmaps, keeping dedicated notebooks, and so forth.
I use paper for almost all my serious reading and primary notetaking. When I read the source document electronically, it's very tempting to just cut and paste entire sections without actually reading and digesting them. Though I could scan my notes and capture them electronically--and do for drawings--typing them in encourages me to be more selective and, again, to actually think about the material first.
Katherine
