Evernote (www.evernote.com) does a terrific job of capturing all kinds of information and can be organized to keep notes for a particular course together. Circus Ponies Notebook is a more notebook-like organizing principle, and creates an index automatically. If you think graphically, Mind Mapping is a terrific way to go, and there are several great mindmapping applications for the Mac--enjoy!
My daughter is coming to the Mac side (my son-in-law came over last summer). She has previously used FileMaker for the PC for her virtual index cards--that is, for taking notes and keeping other information for her books and articles and other academic purposes. FileMaker really isn't the best for the purpose, and she's hoping that there may be some fellow academics among you who have encountered this situation. She is over her head in work and has asked me to present the question to you. Any suggestions?