A first decision is which style to go for. We prefer mindmapping software for brainstorms and presenting information, and Evernote for collecting, structuring and retrieving information.
Of the mind mappers, we recommend four products - MindManager, MindMeister, iThoughtsHD and Freemind. Freemind is free and will give you a feel for mind mapping on a computer before, perhaps going for one of the others. It's also the only one available for Linux. For very easy quick maps, wide access with web use,
mobile/iPad apps and realtime collaboration you can’t beat MindMeister. For the best formatting, particularly if you want to share information with Microsoft Office products, and for a superbly slick look, MindManager has the edge. As a standalone iPad app we like iThoughtsHD.
Evernote is super for general note taking, and we very much recommend it for collecting information as it is so easy to access your info across multiple platforms via the Cloud.
Another category we call idea bubblers, which work best for green field thinking. These tend to be rather like an electronic version of brainstorming with Post-it Notes (though obviously with much more sophistication).
One to try is Creative Thinker, using hexagons to represent and group ideas.
Decision Explorer is a rather different beast, which we can only really recommend if you need its very special capabilities or are a decision support professional.