One of the tools I am using for years now is Tinderbox from Eastgate. I have used it for quite some time to write this weblog here (but swichted to WordPress + MarsEdit recently). Nevertheless I think Tinderbox is a helper in many ways – although there are always features that can be and will be missed.
With a retail price of $229 USD the tool is not cheap – but depending on the usage and potential productivity gain this can be a bargain.
If you are ready and able to write some export templates one can export almost anything to XML or HTML and turn that into layouted documents, presentations or websites.
The “magic” of Tinderbox is that it allows visual unstructured brainstorming and turn that into structured documents over time. But does not stop there like other mind mapping tools: by adding text notes, metadata, agents and actions that perform queries and manipulate data. So you can make your document smarter and add some automatism to it. There are endless ways to use Tinderbox and to make it fit to your brain.
You can’t expect from Tinderbox: online collaboration, custom import of any data, direct export to MS Office documents and the like, table editing within notes, a programmable enviroment (alhtough actions and agents can do a lot already), a Windows version (supposed to be in the making).
Here is a software review by Natan Matias from Sitepoint.