Lucy Gray points to five notetaking applications to help students keep and organize notes from their research. In addition to those mentioned by Lucy, Kairosnews recently pointed to Zotero. Zotero is a free Firefox 2.0 extension/add-on that enables note taking organization from within Firefox.
...helps you gather and organize resources (whether bibliography or the full text of articles), and then lets you to annotate, organize, and share the results of your research. It includes the best parts of older reference manager software (like EndNote)â€”the ability to store full reference information in author, title, and publication fields and to export that as formatted referencesâ€”and the best parts of modern software such as del.icio.us or iTunes, like the ability to sort, tag, and search in advanced ways. Using its unique ability to sense when you are viewing a book, article, or other resource on the web, Zotero willâ€”on many major research sitesâ€”find and automatically save the full reference information for you in the correct fields.