Ever since I began using computers for teaching and writing at the end of the 1970s, I have been hoping for a really good note-taking application. I have tried a lot of them, including making notes on a word processor--easy to type and store, but not so easy to sort.
Farhad Manjoo in the New York Times writes of new note-taking software, and makes a special case for Evernote, which has the advantage of storing notes on the Internet, thereby accessible from any computing platform. Google Notes would do this for you as well, but Google has announced that it is no longer developing the application, and this emphasizes the problem with using any computer application for note-taking -- it needs to stay in business or your notes won't be of any use to you.
Manjoo reports that the best current application is Microsoft's OneNote, but the application is available only for the PC--there is no Mac version. In addition to the applications mentioned by Manjoo , there are of course database applications such as Filemaker, and bibliography programs, such as EndNote. For another free application, I'm also currently exploring Scribe, developed by the Center for History and New Media at George Mason University. CHNM is also the developer for Zotero , which CHNM advertises as a successor application to Scribe, able to handle both bibliographic entries, with web capture, and standalone notes. CHNM has developed a number of other useful applications.
Most of the dedicated note-taking programs are based on one or both of two assumptions -- that the researcher is making notes that copy, comment on, or amplify parts of a published source the primary reference to which is part of a bibliography; or that the notes are being saved as part of a process of clipping from web-based pages. Most of the programs make it possible to take free-standing notes -- something like the old-fashioned 3x5 or 4x6 card -- but that is not the standard metaphor for all of them.
Farhad Manjoo, "Bringing Order to the Chaos of Notes," New York Times, 27 May 2009.