Although I like vim for programming and config file editing, I is not the perfect solution for me for note-taking. I like more markup and a GUI with some functionality. The perfect solution for me is Tomboy[0]. It is included in many Linux distributions and there is an installer for Mac OS and Windows. I love the SSH synchronization mechanism that keeps my notes secure on a virtual hosted server and up to date across my computers.

[0] http://projects.gnome.org/tomboy/