Remember in "Jurassic Park" when the little girl looks at a weird graphical pyramid display and somewhat incongruously says "This is UNIX"? Well, TopicScape 3D Pro ($150, 30-day free trial) may not be Unix, but it does show your data as a series of different-sized pyramids over which you can fly. What impressed me about it is that, unlike many data visualization or "mind mapping" programs, I actually found this one intuitive (mostly) and useful.
Fundamentally, TopicScape Pro is an outliner--you have parent and child topics, and build trees of the relationships between them. The size of each cone is indicative solely of its position and not the number of data pieces, or "occurrences", in contains.
Only metadata is stored in the Topicscape Pro document; all actual data, such as word processor files, spreadsheets, Web links, or movies, remains where it was. Topicscape Pro is all about the relationships between data, and provides a variety of tools to map them. You can, for example, place any given category in multiple places, as a topic may well be the child and/or parent of many other things. Each instance of the topic contains the same data, so it doesn't matter how you get to it. It is also possible to "loosely associate" topics, creating links which are not parent/child, so that you can make general connections which are not hierarchical.
Topicscape Pro is easy to use, but it still has a learning curve. There is an extensive and useful tutorial, but it still took a little poking and reading of the help file to fully grasp everything. For example, at first, I did not understand how to see "inside" a cone without shifting to a full-screen view of the cone's contents. Then I learned to right-click and choose "Show Contents" to have full access to all occurrences in the cone. Other interface issues were similarly minor. Topicscape Pro has its own set of conventions to get used to, mostly because what it does doesn't fall into the standard word processor/spreadsheet/database model.
Is Topicscape Pro for you? If you have a lot of different files and links related to a single project, task, or goal, and you want to be able to quickly find them by their relationship to each other and not by their location on your disk or the Web, Topicscape Pro is an excellent tool. Of course, there are two overheads--learning to use the program and then setting up all the files, entering tags, making associations, and so on. Obviously, it's best to use Topicscape to start organizing your data from the beginning, but it's not always obvious at the start of a project that such a tool is needed. The 30-day full-featured trial should be enough to evaluate its usefulness.