Knoesis — The Right Tools for Research
Software designed to help students (and teachers) conduct research. Offered in three levels, with a free 60 day download of the most basic level. Basically, note cards on the computer. Costs are about $40 – $50 per computers.

The Play of Mind: Software on the History of Ideas
Free software for wide range of ages and wide range of topics. Includes 11 interactive programs divided into four types.

Software designed to help build simple diagrams of complex reasoning. Allows you to create presentations with multiple pages using diagrams, flowcharts, etc. Probably more useful for teachers, but could be used by students for presentations. Includes a free download demonstration version.