I bought today a book by Stefan Klein, called The Secret Pulse of Time. Making Sense of Life's Scarcest Commodity (New York: Marlowe & Company, 2007). It was first published in German in 2006 under the title Zeit. Der Stoff, aus dem das Leben ist. Eine Gebrauchsanleitung, and it is a "good read." I especially like the way in which the author connects recent discoveries in neuroscience with more prosaic things, such as why some people are "morning persons" and others are not.
One of the things that seems to me important in the context of note-taking is his description of an experiment about memory the Dutch psychologist Willem Wagenaar conducted. Beginning in 1978, he would write down every evening one or two of the most interesting events he had experienced that day, using four index cards. On the first he recorded where the event had taken place, on the second when, on the third what kind of an event it was, and on the fourth who was with him. An example might be the consumption of a particularly good bottle of wine. "Six years later, he tested his memory," drawing one of the cards stating the nature of the event (like "enjoyed a good bottle wine"), and then tried to remember what was on the other cards (when, where, with whom). If he could not remember, he would draw a second card, and so on. It turned out that the cards stating the "What?" were most useful, though those with information on "Where?" and "Who?" were also useful. But the "When?" was "useless in every instance" (p. 116).
This seems to show to me that noting down the time at which one has made a note is not important, if we are worried about how best to remember some information. It would also seem to mean that the temporal order of notes, as it would naturally be found in a Notebook or Journal, is not the most effective way to organize information for later recall. Systematic connections of the material seem to be far superior. This is why a hypertextual system, like a personal wiki, might in fact be the best and most "natural" way to store one's notes.
This does not, of course, mean that it is unimportant to store the time when the note was taken. On the contrary, because this is something that we are most likely to forget, a good Note-taking system should record the time when the note was taken, just because this might become important at a later time. Automatic recording of time and any eventual changes might be best, and this is where a program like ConnectedText excels, keeping an automatic record as to when any note was created and revised, allowing you to reconstruct when you took what note or conceived of which idea.