Some time ago, I bought and read Gerald M. Weinberg, Weinberg on Writing. The Fieldstone Method. Since programs which use the index card metaphor may be said to suggest a similar approach, it is perhaps not entirely inappropriate to say a little bit about this "method."
Weinberg starts from the observation of how people in New England and elsewhere build fieldstone walls. They first accumulate a pile of stones, "one or two at a time" without a specific project in mind. In fact, collectors of fieldstones may have several projects going at the same time. At some point, after they have collected enough stones of varying sizes, shapes, colors, texture, and density, they will determine where the particular stones fit in.
Writing can be approached in the same way. We can accumulate ideas or chunks of writing over time without worrying very much about how they will fit into any particular kind of project we have. What is important is that we accumulate the ideas and passages and then later fit them together into something more coherent, but the idea is not to force it.
Weinberg actually suggests the use of note cards for collecting the chunks of writings or the ideas. But there is of course no reason why you could or should not use a blog, an outliner, or a wiki to collect them.
However, if you do use software, the metaphor of "fieldstones" is ultimately just as unimportant as is that of "notecards," though I imagine there is someone somewhere writing on a program that allows you to push around pictures of fielstones that represent ideas because he believes that this will allow you to see better how they "fit." I find Scrivener's and SuperNote's index cards just as superfluous as such "field stones." Though I can also see how visualization might help. Isn't that why most of us use an abacus for counting and basic arithmetic?