Establishing a solid information architecture is the key to a successful SharePoint project, regardless of the type (web content management, enterprise content management, etc.). Over the years I've learned a lot about this from my good friend and fellow MVP Ruven Gotz.
Ruven has done more to promote how to gather and build a solid IA from the business than anyone else in the SharePoint space. His book Practical SharePoint 2010 Information Architecture is an excellent resource, regardless of what version of SharePoint you are using. I also recommend checking out Ruven's blog at http://spinsiders.com/ruveng/.
One of the tools that Ruven introduced me to that all of our Senior Consultants at Envision IT use now is MindJet's MindManager (now just called MindJet). It is a great tool for brainstorming and information planning and organizing. It is not focused on the presentation details of the information, but rather just capturing the ideas and the relationships between them.
For our Envision Shakespeare Company site, we have started to flesh out the information architecture, along with some of the feature and term store ideas. Joe did most of the work on this, and I've included both the PDF and MindJet versions of the files for you to see.
Envision Shakespeare Company Information Architecture.pdf