I've been using Freemind for the past year, and it has been indispensible. I have all of my notes for all of my lectures stored in individual mindmaps. Each of these maps is linked from a top level map. I have been able to include lecture notes, links to Word documents, links to PDF readings, embed diagrams and pictures and link to external URLs. Of course I have many suggestions for improvement, but these are because I love using Freemind so much.