Sometimes we work with some pretty complicated ideas and interwoven concepts. It can make your mind spin. So, one of the ways to beat the confusion is to draw out the ideas through mind mapping.
Here are some links to software that we use for mind mapping. There are two different categories of software that touch on this area. There is concept mapping and mind mapping. One is used more in business and brainstorming while the other, concept mapping, is used more to visualize the sciences.
In my opinion, the best business product is MindJet Mind Manager Pro. Find it at http://www.mindjet.com/default.aspx . They also have a new web based version of their product which is getting good reviews but does cost some money as well. They have educational discounts. so check into that if you like the product. It is one of the most mature out there for the business world.
Best free desktop mind mapping product: Freemind. find them at http://freemind.sourceforge.net/wiki/index.php/Main_Page
Best free web based product: http://www.mind42.com/ This site allows users to simultaneously use and update a mind maps during conference calls as well as chatting through skype. It is easy to use, secure and free.
Best mix of concept mapping with mind mapping is Inspiration. I have also used this in the past and found it helpful. Their focus is on the High School and College educational crowd. Here is their web site: http://www.inspiration.com/
Here is a list of mind mapping software: http://en.wikipedia.org/wiki/List_of_Mind_Mapping_software
Here is a list of concept mapping software: http://en.wikipedia.org/wiki/List_of_concept_mapping_software
You will see that some of these overlap. My general observation is that mind mapping software is much easier to use and is friendlier than concept mapping software which seems to be used mostly be the geek crowd. The geeks do innovative things but you pay for them in learning curve.
If you are new to mind mapping and want some ideas or tips go here..