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FreeMind is a Mind-Mapping tool and an intuitive editor for tree-structured data. The recent development has hopefully turned it into high productivity tool.

Current users of FreeMind use it for the following purposes:

Keeping track of projects, including subtasks, state of subtasks and time recording
Project workplace, including links to necessary files, executables, source of information and of course information
Workplace for internet research using Google and other sources
Keeping a collection of small or middle sized notes with links on some area which expands as needed. Such a collection of notes is sometimes called knowledge base.

Essay writing and brainstorming, using colors to show which essays are open, completed, not yet started etc, using size of nodes to indicate size of essays. I don't have one map for one essay, I have one map for all essays. I move parts of some essays to other when it seems appropriate.
Keeping a small database of something with structure that is either very dynamic or not known in advance. The main disadvantage of such approach when compared to traditional database applications are poor query possibilities, but I use it that way anyway - contacts, recipes, medical records etc. You learn about the structure from the additional data items you enter. For example, different medical records use different structure and you do not have to analyze all the possible structures before you enter the first medical record.

Commented internet favorites or bookmarks, with colors and fonts having the meaning you want.