Zim is pretty decent if you like something on the desktop and like wikis. Its strength is in quickly organizing a bunch of related ideas/notes (being a wiki) but it is much faster to use than a browser-based wiki. http://zim-wiki.org/ I tend to just scribble in Vim though, or use paper and pencil.
I find it to be sort of halfway between Notational Velocity and Evernote. Like nv it stores everything as flat files, but like Evernote you can add some structure to how your organize things.