What do you use to organize your thoughts for a new website o...

balsamiq is great for ui mockup. Other than that I agree with habs, paper works. Although i have recently started using Microsoft One Note 2007. It makes for great brainstorming / idea throwing / white boarding.

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I like to use mindmaps for planning and concept work like this.

Freemind is a good open source mindmap editor for the desktop.

Or you could try my online, browser-based mindmap app. http://thoughtmuse.com ;)

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I'm currently on my second project and for both (and everything else) I use two tools:

Xmind Mind Mapping: I paid like 120 bucks for it, now they decided to open source it (that I did not like much, but now you can get it for free!) Their software is amazing. http://www.xmind.net/

MacJournal: Quick notes, texts, transcripts, voice notes, video notes, etc I have in there. They have full screen writing which is amazing. http://www.marinersoftware.com/sitepage.php?page=85

First stage UIs: Balsamiq. http://www.balsamiq.com/

Final UIs and documentation: Axure Pro (Windows only :( ) (VMWare anyone :) ) http://www.axure.com/

Creating manuals, customer support and FAQ: ScreenSteps. (I cannot recommend this software enough! AMAZING) http://www.bluemangolearning.com/screensteps/

Project Management: Merlin. Fantastic software. http://www.projectwizards.net/en/

Sales and CRM: Daylite. Just started using it. Very powerful, but the learning curve is steep. http://marketcircle.com/

Remote team work: Basecamp and Campfire. www.37signals.com

If everything else fails: a pen and paper :)

Hope this helps

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