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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