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TiddlyWiki - a non-linear personal web notebook
Xmind - Xmind is a brainstorming and mind mapping application.
Personaldb - Note taking with non-linear power
MindMeister - Create, share and collaboratively work on mind maps with MindMeister, the leading online mind mapping software. Includes apps for iPhone, iPad and Android.
Roam Research - A note-taking tool for networked thought
Coggle - Coggle is a simple, beautiful, powerful way of structuring information.