Brainstorming: Organize thinking online

Try an interactive online whiteboard

http://skrbl.com

skrbl is simple and easy, you can start your whiteboard with just one click . Then, click anywhere and type on your skrbl whiteboard. No new tools to learn, nothing to download, nothing to install and you don't even have to sign up. Switch between freehand drawing, and text mode with the click of a button.

Create Timelines:

http://www.readwritethink.org/materials/timeline/index.html

http://timetoast.com

Create and Explore:

http://xtimeline.com/

Example: History of the iPhone:

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Free online Mind Mapping Tools:

Bubbl.us

http://bubbl.us/ 

Mindomo

http://mindomo.com/

Gliffy

http://gliffy.com

mind42

http://www.mind42.com

Websites as graphs (see below for a visualization of this wiki)

http://www.aharef.info/static/htmlgraph/