Here's a pretty neat piece of software: MindMap. A free tool that helps you build visual maps to display and connect information. This is a much more sophisticated version of what I encourage students to do in our methods and analysis course. And you can export it to HTML as well; check out this example: http://freemind.sourceforge.net/PublicMaps.html (you need Java running for this to work). I think it would take a bit of patience to become comfortable with using this, but it would be great for larger research projects or papers. Hat tip: James Fallows at The Atlantic for his article on this and other new tech fun.
On another related note, Fallows writes about how the changing standards of software and data storage over time means that older information, such as documents or digital photos, are lost much more quickly than old-fashioned hardcopies. This isn't a particularly new observation, as various writers and activists have noted. For example, microfilm led to the destruction of newspaper archives around the world, only to have these poor-quality black and white replications themselves begin to deteriorate long before the papers would have. The Library of Congress also has various information on now obsolete technologies that it is hard-pressed to maintain.
Yet I'm not certain that this concern will remain a problem. Certainly older hardware and software standards make archiving difficult. But as more material moves online, it would appear that these networks can undergo improvements while retaining the old information. Discrete information may be threatened (like your 3.5 inch or Zip disk as these drives disappear), but I don't think that one morning Blogger will tell me that they've created a new version and all my old posts are unreadable. Of course, Blogger or Google could have a system crash and lose all that data, but that's a different sort of problem.
The analog might be the development of the rail system. Originally the US ran on several incompatible rail gauges, limiting the ability of trains to function universally across the US. Once that system was standardized, however, trains could run anywhere, and as importantly, the preservation of that network meant that technology was compatible across time. A 100 year old train can run on the rails today, even if it is an anachronism. It seems to me that we are moving toward more unified networks and standards in information, such that future changes will not necessarily mean that we lose our past.