Slatebox is a free tool that you can use to create presentations, mind maps, organize thoughts, and much more. You can create different slates (notes/items) and link and organize them.
There is a free version and it is very easy to use. You can work on slate's collaboratively with others also.
Teachers and students could use this for organizing their thoughts, creating presentations, and mind mapping.
They are working on a version specifically tailored towards education. If you would like to be part of the pilot program, go here: http://slatebox.com/Education
Here's an example of one on energy.
Related:
Popplet - online presentation, mindmapping, and bulletin board
MindMeister - online mind mapping and brain storming
Spicynodes - visualize and organize information and resources
Bubbl.us - online brainstorming for free
Thoughtboxes - organize everything you do - great resource for education
Mindomo - brainstorming and mindmapping software