I'm in the beta team of a very small group of developers that's been building a 3D concept-mapping tool for a couple of years. (If you're familiar with Mind Mapping®, concept mapping has many similarities.) This tool is called Topicscape and we're looking for people interested in trying it out. It is at the Beta 2 stage and has been through a few months of testing by a small group of outside users.
It uses a concept mapping approach because we believe that's a great way to think and plan but it's really a tool for organizing all sorts of information as well as getting your thoughts straight. Each node can have files, URLs, emails and parts of files dropped on it. You can have many files on a node if you want.
We chose to make it work in 3D, because sometimes concept maps (and Mind Maps®) can get too big if you use them on big projects or as a place to organize a lot of reference information. We've found that using 3D on a computer screen allows us to take in and understand much more at a time. It's written mainly in Java because we want it to be multi-platform, but so far it's only working on Windows - Linux and Mac versions will be along when we've converted the drag-and-drop logic that uses features that Java doesn't support (equivalents of OLE and stuff).
It's a personal edition (one PC). If you'd like to try it, the web site is http://www.topicscape.com/. There are screen shots and stories from users showing how they organize their work, personal information and hobbies.
Mind Maps® and Mind Mapping® are registered trademarks of the Buzan organisation.
Topicscape® is a registered trademark of 3D-Scape Limited