Bringing Order to the Chaos of Notes, a recent article in the New York Times, sounds interesting, but is essentially nothing but a list of references to some note-taking programs: OneNote (on the Windows Platform), NoteBook, Yojimbo, and Together (on the Mac), and EverNote as a program that "has many of the functions of the other apps I tried, but that stores your data on the Internet cloud, making it available to you everywhere." One of its strength is that it accepts many different input devices. EverNote gets the most praise: "Your electronic data, meanwhile, is replicated on the Web and on all your machines, and will probably be safe for years. This can make all the difference: With computerized notes, your daily musings are permanent. In time, they could add up to something grand."
I am not sure whether "will probably be safe for years" isn't damning with faint praise. Your notes will be just as permanent as the Website on which they are stored, and that may not be very permanent at all.
I do like a local version of my data with local backups because that way I have more control over them.
I should perhaps also mention that CintaNotes, mentioned in a comment by Anatolica, has a new Beta (M 9.0) out. See CintaNotes. It does much of what EverNote does, but it is a very light weight application that can serve well as an Inbox for your main note-taking application.
I like it.